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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
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