Biostar Beta. Not for public use.
John ♦ 12k
Role: Moderator
Status: New
Handle: @John3139
Reputation: 12180
Email: m*********@gmail.com
Joined: 9 months ago
Last seen: 13 months ago
Location: Germany

Mistakes will be made...

Posts Awards
2
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0
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4.0k
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A: Checking fastq is valid
3.2 years ago
John 12k • updated 10 months ago
RamRS 21k
1
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1
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1.1k
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Calling SNPs on Bisulphite Data
bissnp GATK
4.3 years ago
John 12k • updated 18 months ago
CEB • 0
2
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0
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1.2k
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A: BAM files for RRBS data in ENCODE Project
4.1 years ago
John 12k • updated 18 months ago
RamRS 21k
1
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0
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1.6k
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A: Sort Sequences In A Fasta File According To The peg List
4.1 years ago
John 12k • updated 18 months ago
RamRS 21k
2
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0
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1.1k
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A: "Good" epigenetic histone modification ChIP-seq datasets
4.1 years ago
John 12k • updated 18 months ago
RamRS 21k
2
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0
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1.9k
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A: Check BAMs are complete and clean
4.1 years ago
John 12k • updated 18 months ago
RamRS 21k
0
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0
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1.9k
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C: Check BAMs are complete and clean
4.1 years ago
John 12k • updated 18 months ago
RamRS 21k
7
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6
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1.4k
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Is there an authoritative source for optional BAM tags?
BAM Duplicates MarkDuplicates Picard
4.1 years ago
John 12k • updated 18 months ago
RamRS 21k
1
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1
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1.4k
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A: Is there an authoritative source for optional BAM tags?
4.1 years ago
John 12k • updated 19 months ago
RamRS 21k
0
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1
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1.4k
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C: Is there an authoritative source for optional BAM tags?
4.1 years ago
John 12k • updated 19 months ago
RamRS 21k
0
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1
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4.0k
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C: Questions about multithreading of BWA
4.1 years ago
John 12k • updated 19 months ago
RamRS 21k
1
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0
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8.9k
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A: Check if BAM is derived from pair-end or single-end reads?
3.8 years ago
John 12k • updated 19 months ago
RamRS 21k
0
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0
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2.2k
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C: split bed file into several bed files where each region is separated of any othe
4.1 years ago
John 12k • updated 19 months ago
RamRS 21k
0
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1
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2.2k
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C: split bed file into several bed files where each region is separated of any othe
4.1 years ago
John 12k • updated 19 months ago
RamRS 21k
0
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0
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27k
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A: How To Get Number Of Reads In Bam File Efficiently In Python?
5.1 years ago
John 12k • updated 19 months ago
RamRS 21k
2
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1
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5.9k
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A: cannot import pysam. Module has no attribute error
4.3 years ago
John 12k • updated 19 months ago
RamRS 21k
0
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0
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2.3k
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C: BQSR: when it is applicable?
2.4 years ago
John 12k
1
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1
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2.3k
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C: BQSR: when it is applicable?
2.4 years ago
John 12k
0
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0
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2.3k
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C: BQSR: when it is applicable?
2.4 years ago
John 12k
0
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0
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836
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C: How to tell if a FastQ file is a concatinate of 2 seperate illumina runs?
2.4 years ago
John 12k
0
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1
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836
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C: How to tell if a FastQ file is a concatinate of 2 seperate illumina runs?
2.4 years ago
John 12k
1
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2
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2.3k
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C: BQSR: when it is applicable?
2.4 years ago
John 12k
0
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0
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953
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A: Is there any disease mainly caused by underexpression or overexpression of some
2.5 years ago
John 12k
2
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0
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5.9k
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A: Meaning of BWA-MEM MAPQ values
2.5 years ago
John 12k
0
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0
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3.2k
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C: Amzon EC2 for bioinformatics, genomics, NGS analysis
2.6 years ago
John 12k
0
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1
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2.1k
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C: Declining quality of biostars
2.7 years ago
John 12k
0
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0
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2.2k
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C: BAM to CRAM to BAM
2.7 years ago
John 12k
11
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6
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1.3k
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In-place writable BAM files
bgzip bam
4.1 years ago
John 12k • updated 2.7 years ago
Biostar 20
0
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0
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36k
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C: samtools sorting and indexing
2.8 years ago
John 12k
0
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0
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36k
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C: samtools sorting and indexing
2.8 years ago
John 12k
12
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2
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36k
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A: samtools sorting and indexing
2.8 years ago
John 12k
0
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2
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2.1k
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C: Declining quality of biostars
2.8 years ago
John 12k
1
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0
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1.4k
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C: SAM file size after STAR alignment
2.8 years ago
John 12k
3
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1
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1.3k
Views
C: Where and how NGS techniques are heading for the next 5 years?
2.8 years ago
John 12k
2
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1
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5.6k
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C: Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score doe
2.8 years ago
John 12k
0
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0
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5.6k
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C: Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score doe
2.8 years ago
John 12k
0
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1
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5.6k
Views
C: Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score doe
2.8 years ago
John 12k
1
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0
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5.6k
Views
C: Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score doe
2.8 years ago
John 12k
0
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1
Reply
5.6k
Views
C: Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score doe
2.8 years ago
John 12k
4
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2
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5.6k
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A: Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score doe
2.8 years ago
John 12k
2
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3
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5.6k
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C: Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score doe
2.8 years ago
John 12k
0
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0
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2.0k
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C: Preparation for Bioinformatics.SE closing
2.8 years ago
John 12k
0
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0
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2.0k
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C: Preparation for Bioinformatics.SE closing
2.8 years ago
John 12k
0
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0
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1.3k
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C: Keeping Tags That Are Mapped To The Same Place By Two Aligners
2.8 years ago
John 12k
2
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1
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2.0k
Views
C: Why bioinformaticians need to know programming languages?
2.8 years ago
John 12k
2
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0
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2.0k
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C: Why bioinformaticians need to know programming languages?
2.8 years ago
John 12k
0
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1
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2.0k
Views
C: Why bioinformaticians need to know programming languages?
2.8 years ago
John 12k
2
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1
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2.0k
Views
A: Why bioinformaticians need to know programming languages?
2.8 years ago
John 12k
69
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39
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2.0k
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Preparation for Bioinformatics.SE closing
biostars Forum
2.8 years ago
John 12k • updated 2.8 years ago
me • 690
0
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0
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2.0k
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C: Preparation for Bioinformatics.SE closing
2.8 years ago
John 12k
1
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1
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2.0k
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C: Preparation for Bioinformatics.SE closing
2.8 years ago
John 12k
0
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0
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1.9k
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C: Poll: How many people have PyPy?
2.9 years ago
John 12k
0
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1
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1.9k
Views
C: Poll: How many people have PyPy?
2.9 years ago
John 12k
2
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0
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1.5k
Views
C: uQ - small binary FASTQ
2.9 years ago
John 12k
33
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26
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1.9k
Views
Poll: How many people have PyPy?
pypy python Forum
2.9 years ago
John 12k
2
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1
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5.4k
Views
C: Lossless ALAPY Fastq Compressor (now with stdin/stdout support)
2.9 years ago
John 12k
2
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1
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865
Views
C: why does this pipe work
2.9 years ago
John 12k
0
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1
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778
Views
C: Collaboration on an empirical QC tool
2.9 years ago
John 12k
2
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1
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778
Views
A: Collaboration on an empirical QC tool
2.9 years ago
John 12k
2
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0
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865
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A: why does this pipe work
2.9 years ago
John 12k
7
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1
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2.1k
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A: Good practices while dealing with very large datasets
2.9 years ago
John 12k
1
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1
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2.1k
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C: Good practices while dealing with very large datasets
2.9 years ago
John 12k
0
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1
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2.1k
Views
C: Good practices while dealing with very large datasets
2.9 years ago
John 12k
2
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0
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1.1k
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C: A long run time problem
2.9 years ago
John 12k
0
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0
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2.4k
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C: Programming language use distribution from recent programs / articles
2.9 years ago
John 12k
5
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0
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2.4k
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C: Programming language use distribution from recent programs / articles
2.9 years ago
John 12k
1
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2
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2.4k
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C: Programming language use distribution from recent programs / articles
2.9 years ago
John 12k
0
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0
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525
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C: Getting my head around the Pymol documentation brackets
2.9 years ago
John 12k
0
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0
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1.2k
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C: Malformed BAM file produced by BWA
2.9 years ago
John 12k
0
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0
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1.9k
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C: GATK on RNASeq/ChIP data - distinction between no SNP and no data.
2.9 years ago
John 12k
1
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0
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1.3k
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C: DNA fragmentation is biased
3.0 years ago
John 12k
2
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1
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1.3k
Views
C: DNA fragmentation is biased
3.0 years ago
John 12k
0
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0
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7.3k
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C: pybam - 100% python BAM reader
3.0 years ago
John 12k
1
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1
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7.3k
Views
A: pybam - 100% python BAM reader
3.0 years ago
John 12k
37
Votes
20
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7.3k
Views
pybam - 100% python BAM reader
python bam pysam htspython Tool
3.0 years ago
John 12k
0
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0
Replies
1.3k
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C: It's about the journey, and not the destination
3.0 years ago
John 12k
0
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1
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964
Views
A: SAM to BAM conversion issues
3.0 years ago
John 12k
1
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0
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13k
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C: Tools to view fastq file
3.0 years ago
John 12k
1
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0
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1.3k
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A: identification of adapters from fastq file.
3.0 years ago
John 12k • updated 3.0 years ago
WouterDeCoster 39k
4
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2
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1.5k
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A: What to use after Salmon
3.0 years ago
John 12k
4
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1
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961
Views
C: Does jellyfish 2 support kmer size > 31
3.0 years ago
John 12k
0
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1
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1.2k
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C: getting the unmapped reads from BAM file
3.0 years ago
John 12k
0
Votes
0
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977
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C: basic concepts behind --sjdbOverhang (STAR)
3.0 years ago
John 12k
0
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1
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977
Views
A: basic concepts behind --sjdbOverhang (STAR)
3.1 years ago
John 12k
2
Votes
0
Replies
606
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C: What is the current price of a bioinfo group?
3.1 years ago
John 12k
0
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1
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1.2k
Views
C: getting the unmapped reads from BAM file
3.1 years ago
John 12k
0
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0
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1.2k
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C: getting the unmapped reads from BAM file
3.1 years ago
John 12k
0
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0
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1.2k
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C: getting the unmapped reads from BAM file
3.1 years ago
John 12k
0
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0
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984
Views
C: Meta-analysis: How to join data from different platforms
3.1 years ago
John 12k
0
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1
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841
Views
C: Bismark on sample with 2 genomes
3.1 years ago
John 12k
0
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1
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841
Views
C: Bismark on sample with 2 genomes
3.1 years ago
John 12k
0
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0
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1.5k
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C: uQ - small binary FASTQ
3.1 years ago
John 12k
6
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1
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988
Views
A: How do you perform functional testing for your Bioinformatics tools?
3.1 years ago
John 12k
1
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1
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1.1k
Views
C: Error of bam-to-sam conversion using samtools
3.1 years ago
John 12k
0
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0
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1.5k
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C: uQ - small binary FASTQ
3.1 years ago
John 12k
18
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21
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1.5k
Views
uQ - small binary FASTQ
FASTQ Compression Tool
3.1 years ago
John 12k
0
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0
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2.3k
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C: Biopython error message: Protein FASTA provided for nucleotide sequence
3.1 years ago
John 12k
1
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0
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1.5k
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C: uQ (again) - binary FASTQ
3.1 years ago
John 12k
1
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0
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1.6k
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A: bam stats F1F2/F1R2/R1F2/R1R2/F2F1/F2R1/R2F1/R2R1
3.1 years ago
John 12k
0
Votes
3
Replies
841
Views
C: Bismark on sample with 2 genomes
3.1 years ago
John 12k
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