Biostar Beta. Not for public use.
Latest
Topics
Tags
News
Jobs
Tutorials
Forum
Planet
Community
New Post
Log In
About
New Post
Latest
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit to: all time
all time
today
this week
this month
this year
1,157 results • Page
1 of 24
Sort by: Rank
Rank
Views
Votes
Replies
Showing :
bam
•
reset
0
Votes
1
Reply
107
Views
Available tools that can pick up the the alignment with highest mapping quality
bam
mapping quality
19 months ago
gerrybio2010
• 0
• updated 19 months ago
WouterDeCoster
39k
1
Vote
11
Replies
254
Views
Fastq to BAM
bam
fastq
19 months ago
zliew
• 0
21
Votes
18
Replies
1.2k
Views
Tool:
elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
sam
bam
markduplicates
sort
bqsr
Tool
19 months ago
Charlotte.Herzeel
• 140
0
Votes
1
Reply
190
Views
Merging BAM file with Samtools
samtools
merge
BAM
20 months ago
seta
♦ 1.2k
• updated 20 months ago
Devon Ryan
90k
1
Vote
0
Replies
162
Views
Confused about read pair orientation in bam
alignment
bam
bwa
paired end
20 months ago
malthesr
• 10
0
Votes
3
Replies
175
Views
How to tell whether a bam file is "analysis-ready" (as defined by GATK)?
bam
gatk
bestpractice
20 months ago
minimax
• 0
0
Votes
3
Replies
191
Views
scRNAseq: Split FASTQ into cell specific FASTQ Files
RNA-Seq
Cell Ranger
Split
Demultiplex
BAM
20 months ago
niklas.lang
• 0
3
Votes
4
Replies
164
Views
Getting only Indels and no SNPs after variant calling variant calling using HaplotypeCaller
RNA-Seq
BAM
SNP
GATK
Variant Calling
20 months ago
Susmita Mandal
• 40
0
Votes
1
Reply
129
Views
FastQC Failed to create archive: null
sequence
qc
bam
java
fastqc
20 months ago
jason.williams
• 0
1
Vote
1
Reply
176
Views
Read TCGA BAM files into TEtranscripts tool (python) without downloading them?
TCGA
bam
linux
RNA-seq
20 months ago
Gema Sanz
• 70
5
Votes
2
Replies
194
Views
How does bedtools bamtobed calculate end position
bed
bam
bedtools
20 months ago
6timings
• 0
• updated 20 months ago
John Marshall
♦ 1.5k
0
Votes
0
Replies
147
Views
View MAF file and the reference sequence in a genome viewer/annotator along with SAM/BAM?
SAM
BAM
MAF
viewer
21 months ago
DanielC
• 80
12
Votes
13
Replies
9.1k
Views
6 follow
Comparing And Plotting Coverage Between Two Bam Files
bam
coverage
genome
chromosome
8.6 years ago
Rubal7
• 760
• updated 21 months ago
john.e.major.jr
• 0
1
Vote
2
Replies
166
Views
How to split both bam files and annotation files as per chromosome number?
split
bam
sam
chr
annotation
21 months ago
Glory Basumata
• 140
0
Votes
1
Reply
234
Views
Extracting CIGAR string from a specific region of a read in a bam file using pysam?
pysam
RNA-Seq
BAM
CIGAR
21 months ago
kiki4133
• 0
6
Votes
9
Replies
238
Views
How to separate chrY from a WGS vcf file?
tabix
dantelabs
wgs
yfull
bam
21 months ago
krt
• 0
1
Vote
5
Replies
332
Views
SNP calling with SAMtools on multiple samples
SNP
samtools
vcf
bam
21 months ago
madeira.ag
• 0
• updated 21 months ago
Begali
• 0
12
Votes
7
Replies
2.8k
Views
Trying To Pull Regions From An Online Bam File Without Downloading
samtools
igv
bam
8.5 years ago
Wjeck
• 480
• updated 21 months ago
Biostar
20
1
Vote
4
Replies
273
Views
Filtering BAM file to include PE reads that did not map, even though their mate did
BAM
samtools
filter
mapping
read
21 months ago
nute11a
• 0
• updated 21 months ago
Istvan Albert
87k
0
Votes
2
Replies
218
Views
How to get output with read counts and read count percentages from bam file?
read counts
bam
samtools
picard
22 months ago
bayramliaziz
• 0
• updated 22 months ago
WouterDeCoster
39k
5
Votes
10
Replies
313
Views
Subsampling one bamfile multiple times?
sequencing
bam
subsample
22 months ago
wjdgmlcjf
• 0
3
Votes
7
Replies
270
Views
Bam file MC tag as integer
ValidateSamFile
bam
sam
MC
22 months ago
chariko
• 30
3
Votes
5
Replies
269
Views
How to find a variant in a particular position in a bam file only using samtools
bam
sam
samtools
22 months ago
tw617
• 30
• updated 22 months ago
swbarnes2
5.7k
4
Votes
2
Replies
236
Views
Convert 2 SE bam to PE bam (alignment BWA mem)
alignment
bam
bwa
23 months ago
mynameliuxiang
• 0
• updated 22 months ago
zx8754
7.5k
0
Votes
4
Replies
356
Views
Bam header editing
bam
header
22 months ago
Huynh Nguyen
• 0
• updated 22 months ago
Istvan Albert
87k
0
Votes
2
Replies
174
Views
Read In Function for BAM file processing
Script
BAM
22 months ago
Jonas.Koch
• 0
3
Votes
7
Replies
285
Views
Extract coverage from each nucleotide position of a genome in a bam file
bam
bed
coverage
22 months ago
MAPK
♦ 1.4k
1
Vote
1
Reply
228
Views
How do get additional bam statistics
RNA-Seq
alignment
bam
samtools
22 months ago
t-jim
• 30
8
Votes
12
Replies
377
Views
How to report genomic intervals essentailly overlapping in all files?
bedtools
bed
bam
22 months ago
Vijay Lakhujani
4.1k
3
Votes
8
Replies
259
Views
Find common reads between two bam files
sequencing
bam
reads
22 months ago
yp19
• 20
• updated 22 months ago
Pierre Lindenbaum
120k
11
Votes
0
Replies
435
Views
Tutorial:
Generating consensus sequence from bam file
bam
fasta
consensus
Tutorial
22 months ago
finswimmer
11k
• updated 22 months ago
WouterDeCoster
39k
1
Vote
2
Replies
337
Views
How treat a Bam file with mutiple read groups (RG)
next-gen
BAM
GATK
picard
read group
22 months ago
zamani_2012
• 0
• updated 22 months ago
Pierre Lindenbaum
120k
3
Votes
3
Replies
358
Views
RNA-Seq QC for aligned files (bam)
RNA-Seq
bam
qc
22 months ago
genomics Newbie
• 20
• updated 22 months ago
Friederike
4.2k
1
Vote
2
Replies
227
Views
Might @PG headers affect downstream analyses, and how can I safely remove them from a BAM file?
bam
@PG
read groups
22 months ago
olikidrod
• 0
• updated 22 months ago
h.mon
25k
17
Votes
28
Replies
565
Views
collapsing transcript expression to gene-level expression
FeatureCounts
BAM
RNA-Seq
22 months ago
F
♦ 3.4k
1
Vote
3
Replies
257
Views
Subsampling aligned SAM/BAM files for RNA-seq analysis
RNA-Seq
subsampling
downsampling
SAM
BAM
23 months ago
mohammedtoufiq91
• 40
• updated 23 months ago
WouterDeCoster
39k
4
Votes
4
Replies
245
Views
How to remove bam files that don't contain matching reads
bowtie2
samtools
BAM
23 months ago
samlambrechts299
• 130
• updated 23 months ago
Pierre Lindenbaum
120k
2
Votes
5
Replies
249
Views
Should I remove duplicates?
BAM
Duplicates
next-gen
23 months ago
F
♦ 3.4k
• updated 23 months ago
ATpoint
17k
1
Vote
6
Replies
207
Views
Seeing only "N's" in tablet genome viewer?
genome
viewer
bam
23 months ago
tuj92050
• 0
2
Votes
4
Replies
320
Views
Extracting a chromosome from an indexed bam file?
bam
chromosome
samtools
23 months ago
tuj92050
• 0
2
Votes
1
Reply
1.4k
Views
Bam File With Maq
bam
9.4 years ago
Sara
• 130
• updated 23 months ago
Biostar
20
0
Votes
3
Replies
269
Views
Count matrix showing different results than UCSC tracks
ucsc
featurecounts
bigwig
bam
mm10
23 months ago
raquelgarza95
• 40
0
Votes
3
Replies
276
Views
Convert BAM files to paired end FASTQ
Samtools
BAM
FASTQ
23 months ago
berke.toptas
• 0
• updated 23 months ago
JC
7.9k
3
Votes
5
Replies
232
Views
Remove duplicate readnames from a bam file
atac-seq
duplicates
BAM
duplicate read names
23 months ago
garnerim1988
• 0
0
Votes
0
Replies
215
Views
From mpileup on bam files to TMB calculation, how is it done?
mutations
TMB
snps
bam
mpileup
23 months ago
Pin.Bioinf
• 240
0
Votes
0
Replies
183
Views
Fixing inconsistent flags (strand info set for only one read) between RNA-seq read pairs with samtools/picard
RNA-Seq
bam
picard
samtools
fixmate
23 months ago
ophilia30092
• 0
0
Votes
4
Replies
289
Views
Understanding the SA tag, Samtools FLAG, and Chimeric Alignments
alignment
bam
23 months ago
nzs208
• 0
0
Votes
6
Replies
2.7k
Views
How do I calculate the total read depth and allele frequency using just the target bed file and aligned bam
bam
bed
mpileup
allele
frequency
5.6 years ago
bobrowdy123
• 0
• updated 23 months ago
Biostar
20
7
Votes
7
Replies
177
Views
Detecting Klinefelter from genomic files
klinefelter
vcf
bam
fastq
23 months ago
paulcaiella
• 0
2
Votes
3
Replies
196
Views
Identify deletion in multiple bam files compared to the same bacterial reference
bedtools
bam
23 months ago
David
• 150
1,157 results • Page
1 of 24
Recent Votes
Phyla Amphora2 test problem
Phyla Amphora2 test problem
Comment: Testing image upload
Testing spam
Random SNPs simulation?
How do play audio (playsound) in background of Python script?
A: Random SNPs simulation?
Biostar Forum Posting Guidelines
Answer: How to install CRISPRCasFinder under Ubuntu without having administrator rights?
Answer: How to install CRISPRCasFinder under Ubuntu without having administrator rights?
Recent Locations
• All
texas,
6 hours ago
China,
23 hours ago
India,
1 day ago
University Park,
1 day ago
Ho Chi Minh, Viet Nam,
1 day ago
Recent Awards
• All
Appreciated
to
lieven.sterck
5.1k
Commentator
to
maegsul
• 140
Appreciated
to
Sej Modha
4.2k
Appreciated
to
Sej Modha
4.2k
Appreciated
to
Sej Modha
4.2k
Appreciated
to
Sej Modha
4.2k
Appreciated
to
finswimmer
11k
Appreciated
to
finswimmer
11k
Appreciated
to
finswimmer
11k
Appreciated
to
finswimmer
11k
Recent Replies
Answer: Testing recipe link
by
khosango
• 0
can't see it hiim ducking from [san go][1] [1]: https://www.khosango.com/
Comment: Python and data science course training Hyderabad
by
Datasciencekphp
• 0
Hi Good evening! Thanks for sharing such nice information about your blog. https://socialprachar.com/data-science/
Comment: Meta: Markdown in Biostars (now enabled)
by
Arup Ghosh
♦ 1.3k
@arup take a look at this.
Answer: Biostar Forum Posting Guidelines
by
макс
• 0
[LD Blue][1] is a light cigarette. The cigarette contains: resin - 6 mg, nicotine - 0.4 mg. There are 20 cigarettes in the pack. The struc…
Answer: Biostar Forum Posting Guidelines
by
sapopi3741
• 0
@Tom Koerber6
Comment: Biostar Forum Posting Guidelines
by
Arup Ghosh
♦ 1.3k
@arup @Tom Koerber6 @Biostar1
Answer: Biostar Forum Posting Guidelines
by
Arup Ghosh
♦ 1.3k
@Tom Koerber6
Comment: Biostar Forum Posting Guidelines
by
Arup Ghosh
♦ 1.3k
@Zhenhai Zhang5
Answer: Biostar Forum Posting Guidelines
by
Arup Ghosh
♦ 1.3k
@Test3895
Answer: Biostar Forum Posting Guidelines
by
Arup Ghosh
♦ 1.3k
This a test answer.
Answer: Phyla Amphora2 test problem
by
Arup Ghosh
♦ 1.3k
@D. Puthier486
Answer: Phyla Amphora2 test problem
by
aurozen
• 0
Are you finding a [cheap gym near me][1] at [gyms in Gwalior][2]? Aurozen helps you to find the nearest gym to maintain [health and fitness…
Answer: KOBAS server is down
by
hasithalee
• 0
This is good topic. **[Narrative Conventions][1]** [1]: https://www.totalassignmenthelp.com/blog/narrative-conventions/
Answer: Biostar Forum Posting Guidelines
by
marieclaimer
• 0
HP Printer Problems We have the necessary tools and manuals to guide and fix HP printer errors. With our professional skills and excellent…
Answer: Biostar Forum Posting Guidelines
by
wasifrazakhan05
• 0
[AOL Mail][1] [trend micro login][2] [mail.aol.com][3] [Magellan GPS update][4] [Norton.com/setup][5] [bitdefender login][6] [garmin …
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.3