Biostar Beta. Not for public use.
John ♦ 12k
Role: Moderator
Status: New
Handle: @John3139
Reputation: 12180
Email: m*********@gmail.com
Joined: 15 months ago
Last seen: 19 months ago
Location: Germany

Mistakes will be made...

Posts Awards
Show
all questions tools blogs news tutorials forum answers comments
2
Votes
0
Replies
4.0k
Views
Answer: A: Checking fastq is valid
3.7 years ago
John 12k • updated 16 months ago
RamRS 21k
1
Vote
1
Reply
1.1k
Views
Calling SNPs on Bisulphite Data
bissnp GATK
4.8 years ago
John 12k • updated 2.0 years ago
CEB • 0
2
Votes
0
Replies
1.2k
Views
Answer: A: BAM files for RRBS data in ENCODE Project
4.6 years ago
John 12k • updated 2.0 years ago
RamRS 21k
1
Vote
0
Replies
1.6k
Views
Answer: A: Sort Sequences In A Fasta File According To The peg List
4.6 years ago
John 12k • updated 2.0 years ago
RamRS 21k
2
Votes
0
Replies
1.1k
Views
Answer: A: "Good" epigenetic histone modification ChIP-seq datasets
4.6 years ago
John 12k • updated 2.0 years ago
RamRS 21k
2
Votes
0
Replies
1.9k
Views
Answer: A: Check BAMs are complete and clean
4.6 years ago
John 12k • updated 2.0 years ago
RamRS 21k
0
Votes
0
Replies
1.9k
Views
Comment: C: Check BAMs are complete and clean
4.6 years ago
John 12k • updated 2.0 years ago
RamRS 21k
7
Votes
6
Replies
1.4k
Views
Is there an authoritative source for optional BAM tags?
BAM Duplicates MarkDuplicates Picard
4.6 years ago
John 12k • updated 2.0 years ago
RamRS 21k
1
Vote
1
Reply
1.4k
Views
Answer: A: Is there an authoritative source for optional BAM tags?
4.6 years ago
John 12k • updated 2.0 years ago
RamRS 21k
0
Votes
1
Reply
1.4k
Views
Comment: C: Is there an authoritative source for optional BAM tags?
4.6 years ago
John 12k • updated 2.0 years ago
RamRS 21k
0
Votes
1
Reply
4.0k
Views
Comment: C: Questions about multithreading of BWA
4.6 years ago
John 12k • updated 2.0 years ago
RamRS 21k
1
Vote
0
Replies
8.9k
Views
Answer: A: Check if BAM is derived from pair-end or single-end reads?
4.3 years ago
John 12k • updated 2.0 years ago
RamRS 21k
0
Votes
0
Replies
2.2k
Views
Comment: C: split bed file into several bed files where each region is separated of any othe
4.6 years ago
John 12k • updated 2.0 years ago
RamRS 21k
0
Votes
1
Reply
2.2k
Views
Comment: C: split bed file into several bed files where each region is separated of any othe
4.6 years ago
John 12k • updated 2.0 years ago
RamRS 21k
0
Votes
0
Replies
27k
Views
Answer: A: How To Get Number Of Reads In Bam File Efficiently In Python?
5.6 years ago
John 12k • updated 2.1 years ago
RamRS 21k
2
Votes
1
Reply
5.9k
Views
Answer: A: cannot import pysam. Module has no attribute error
4.8 years ago
John 12k • updated 2.1 years ago
RamRS 21k
0
Votes
0
Replies
2.3k
Views
Comment: C: BQSR: when it is applicable?
2.9 years ago
John 12k
1
Vote
1
Reply
2.3k
Views
Comment: C: BQSR: when it is applicable?
2.9 years ago
John 12k
0
Votes
0
Replies
2.3k
Views
Comment: C: BQSR: when it is applicable?
2.9 years ago
John 12k
0
Votes
0
Replies
843
Views
Comment: C: How to tell if a FastQ file is a concatinate of 2 seperate illumina runs?
2.9 years ago
John 12k
0
Votes
1
Reply
843
Views
Comment: C: How to tell if a FastQ file is a concatinate of 2 seperate illumina runs?
2.9 years ago
John 12k
1
Vote
2
Replies
2.3k
Views
Comment: C: BQSR: when it is applicable?
2.9 years ago
John 12k
0
Votes
0
Replies
965
Views
Answer: A: Is there any disease mainly caused by underexpression or overexpression of some
3.0 years ago
John 12k
2
Votes
0
Replies
5.9k
Views
Answer: A: Meaning of BWA-MEM MAPQ values
3.0 years ago
John 12k
0
Votes
0
Replies
3.2k
Views
Comment: C: Amzon EC2 for bioinformatics, genomics, NGS analysis
3.1 years ago
John 12k
0
Votes
1
Reply
2.2k
Views
Comment: C: Declining quality of biostars
3.2 years ago
John 12k
0
Votes
0
Replies
2.2k
Views
Comment: C: BAM to CRAM to BAM
3.2 years ago
John 12k
11
Votes
6
Replies
1.3k
Views
In-place writable BAM files
bgzip bam
4.6 years ago
John 12k • updated 3.2 years ago
Biostar 20
0
Votes
0
Replies
36k
Views
Comment: C: samtools sorting and indexing
3.2 years ago
John 12k
0
Votes
0
Replies
36k
Views
Comment: C: samtools sorting and indexing
3.2 years ago
John 12k
12
Votes
2
Replies
36k
Views
Answer: A: samtools sorting and indexing
3.2 years ago
John 12k
0
Votes
2
Replies
2.2k
Views
Comment: C: Declining quality of biostars
3.2 years ago
John 12k
1
Vote
0
Replies
1.4k
Views
Comment: C: SAM file size after STAR alignment
3.3 years ago
John 12k
3
Votes
1
Reply
1.3k
Views
Comment: C: Where and how NGS techniques are heading for the next 5 years?
3.3 years ago
John 12k
2
Votes
1
Reply
5.6k
Views
Comment: C: Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score doe
3.3 years ago
John 12k
0
Votes
0
Replies
5.6k
Views
Comment: C: Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score doe
3.3 years ago
John 12k
0
Votes
1
Reply
5.6k
Views
Comment: C: Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score doe
3.3 years ago
John 12k
1
Vote
0
Replies
5.6k
Views
Comment: C: Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score doe
3.3 years ago
John 12k
0
Votes
1
Reply
5.6k
Views
Comment: C: Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score doe
3.3 years ago
John 12k
4
Votes
2
Replies
5.6k
Views
Answer: A: Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score doe
3.3 years ago
John 12k
2
Votes
3
Replies
5.6k
Views
Comment: C: Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score doe
3.3 years ago
John 12k
0
Votes
0
Replies
2.0k
Views
Comment: C: Preparation for Bioinformatics.SE closing
3.3 years ago
John 12k
0
Votes
0
Replies
2.0k
Views
Comment: C: Preparation for Bioinformatics.SE closing
3.3 years ago
John 12k
0
Votes
0
Replies
1.3k
Views
Answer: C: Keeping Tags That Are Mapped To The Same Place By Two Aligners
3.3 years ago
John 12k
2
Votes
1
Reply
2.0k
Views
Comment: C: Why bioinformaticians need to know programming languages?
3.3 years ago
John 12k
2
Votes
0
Replies
2.0k
Views
Comment: C: Why bioinformaticians need to know programming languages?
3.3 years ago
John 12k
0
Votes
1
Reply
2.0k
Views
Comment: C: Why bioinformaticians need to know programming languages?
3.3 years ago
John 12k
2
Votes
1
Reply
2.0k
Views
Answer: A: Why bioinformaticians need to know programming languages?
3.3 years ago
John 12k
69
Votes
39
Replies
2.0k
Views
Forum: Preparation for Bioinformatics.SE closing
biostars Forum
3.3 years ago
John 12k • updated 3.3 years ago
me • 690
0
Votes
0
Replies
2.0k
Views
Comment: C: Preparation for Bioinformatics.SE closing
3.3 years ago
John 12k
1
Vote
1
Reply
2.0k
Views
Comment: C: Preparation for Bioinformatics.SE closing
3.3 years ago
John 12k
0
Votes
0
Replies
2.0k
Views
Comment: C: Poll: How many people have PyPy?
3.4 years ago
John 12k
0
Votes
1
Reply
2.0k
Views
Comment: C: Poll: How many people have PyPy?
3.4 years ago
John 12k
2
Votes
0
Replies
1.6k
Views
Comment: C: uQ - small binary FASTQ
3.4 years ago
John 12k
33
Votes
26
Replies
2.0k
Views
Forum: Poll: How many people have PyPy?
pypy python Forum
3.4 years ago
John 12k
2
Votes
1
Reply
5.5k
Views
Comment: C: Lossless ALAPY Fastq Compressor (now with stdin/stdout support)
3.4 years ago
John 12k
2
Votes
1
Reply
879
Views
Comment: C: why does this pipe work
3.4 years ago
John 12k
0
Votes
1
Reply
788
Views
Comment: C: Collaboration on an empirical QC tool
3.4 years ago
John 12k
2
Votes
1
Reply
788
Views
Answer: A: Collaboration on an empirical QC tool
3.4 years ago
John 12k
2
Votes
0
Replies
879
Views
Answer: A: why does this pipe work
3.4 years ago
John 12k
7
Votes
1
Reply
2.1k
Views
Answer: A: Good practices while dealing with very large datasets
3.4 years ago
John 12k
1
Vote
1
Reply
2.1k
Views
Comment: C: Good practices while dealing with very large datasets
3.4 years ago
John 12k
0
Votes
1
Reply
2.1k
Views
Comment: C: Good practices while dealing with very large datasets
3.4 years ago
John 12k
2
Votes
0
Replies
1.1k
Views
Comment: C: A long run time problem
3.4 years ago
John 12k
0
Votes
0
Replies
2.5k
Views
Comment: C: Programming language use distribution from recent programs / articles
3.4 years ago
John 12k
5
Votes
0
Replies
2.5k
Views
Comment: C: Programming language use distribution from recent programs / articles
3.4 years ago
John 12k
1
Vote
2
Replies
2.5k
Views
Answer: C: Programming language use distribution from recent programs / articles
3.4 years ago
John 12k
0
Votes
0
Replies
534
Views
Comment: C: Getting my head around the Pymol documentation brackets
3.4 years ago
John 12k
0
Votes
0
Replies
1.2k
Views
Comment: C: Malformed BAM file produced by BWA
3.4 years ago
John 12k
0
Votes
0
Replies
1.9k
Views
Comment: C: GATK on RNASeq/ChIP data - distinction between no SNP and no data.
3.4 years ago
John 12k
1
Vote
0
Replies
1.3k
Views
Comment: C: DNA fragmentation is biased
3.4 years ago
John 12k
2
Votes
1
Reply
1.3k
Views
Comment: C: DNA fragmentation is biased
3.4 years ago
John 12k
0
Votes
0
Replies
7.3k
Views
Comment: C: pybam - 100% python BAM reader
3.4 years ago
John 12k
1
Vote
1
Reply
7.3k
Views
Answer: A: pybam - 100% python BAM reader
3.4 years ago
John 12k
37
Votes
20
Replies
7.3k
Views
Tool: pybam - 100% python BAM reader
python bam pysam htspython Tool
3.4 years ago
John 12k
0
Votes
0
Replies
1.4k
Views
Comment: C: It's about the journey, and not the destination
3.5 years ago
John 12k
0
Votes
1
Reply
979
Views
Answer: A: SAM to BAM conversion issues
3.5 years ago
John 12k
1
Vote
0
Replies
13k
Views
Comment: C: Tools to view fastq file
3.5 years ago
John 12k
1
Vote
0
Replies
1.3k
Views
Answer: A: identification of adapters from fastq file.
3.5 years ago
John 12k • updated 3.5 years ago
WouterDeCoster 39k
4
Votes
2
Replies
1.5k
Views
Answer: A: What to use after Salmon
3.5 years ago
John 12k
4
Votes
1
Reply
972
Views
Answer: C: Does jellyfish 2 support kmer size > 31
3.5 years ago
John 12k
0
Votes
1
Reply
1.3k
Views
Comment: C: getting the unmapped reads from BAM file
3.5 years ago
John 12k
0
Votes
0
Replies
991
Views
Comment: C: basic concepts behind --sjdbOverhang (STAR)
3.5 years ago
John 12k
0
Votes
1
Reply
991
Views
Answer: A: basic concepts behind --sjdbOverhang (STAR)
3.5 years ago
John 12k
2
Votes
0
Replies
617
Views
Comment: C: What is the current price of a bioinfo group?
3.5 years ago
John 12k
0
Votes
1
Reply
1.3k
Views
Comment: C: getting the unmapped reads from BAM file
3.5 years ago
John 12k
0
Votes
0
Replies
1.3k
Views
Comment: C: getting the unmapped reads from BAM file
3.5 years ago
John 12k
0
Votes
0
Replies
1.3k
Views
Comment: C: getting the unmapped reads from BAM file
3.5 years ago
John 12k
0
Votes
0
Replies
997
Views
Comment: C: Meta-analysis: How to join data from different platforms
3.5 years ago
John 12k
0
Votes
1
Reply
864
Views
Comment: C: Bismark on sample with 2 genomes
3.5 years ago
John 12k
0
Votes
1
Reply
864
Views
Comment: C: Bismark on sample with 2 genomes
3.5 years ago
John 12k
0
Votes
0
Replies
1.6k
Views
Comment: C: uQ - small binary FASTQ
3.6 years ago
John 12k
6
Votes
1
Reply
1.0k
Views
Answer: A: How do you perform functional testing for your Bioinformatics tools?
3.6 years ago
John 12k
1
Vote
1
Reply
1.2k
Views
Comment: C: Error of bam-to-sam conversion using samtools
3.6 years ago
John 12k
0
Votes
0
Replies
1.6k
Views
Comment: C: uQ - small binary FASTQ
3.6 years ago
John 12k
18
Votes
21
Replies
1.6k
Views
Tool: uQ - small binary FASTQ
FASTQ Compression Tool
3.6 years ago
John 12k
0
Votes
0
Replies
2.3k
Views
Comment: C: Biopython error message: Protein FASTA provided for nucleotide sequence
3.6 years ago
John 12k
1
Vote
0
Replies
1.6k
Views
Comment: C: uQ (again) - binary FASTQ
3.6 years ago
John 12k
1
Vote
0
Replies
1.6k
Views
Answer: A: bam stats F1F2/F1R2/R1F2/R1R2/F2F1/F2R1/R2F1/R2R1
3.6 years ago
John 12k
0
Votes
3
Replies
864
Views
Comment: C: Bismark on sample with 2 genomes
3.6 years ago
John 12k
Powered by the version 2.3.1