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Showing : bam • reset
0
Votes
1
Reply
104
Views
Available tools that can pick up the the alignment with highest mapping quality
bam mapping quality
13 months ago
gerrybio2010 • 0 • updated 13 months ago
WouterDeCoster 39k
1
Vote
11
Replies
243
Views
Fastq to BAM
bam fastq
13 months ago
zliew • 0
21
Votes
18
Replies
1.2k
Views
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
13 months ago
Charlotte.Herzeel • 140
0
Votes
1
Reply
185
Views
Merging BAM file with Samtools
samtools merge BAM
13 months ago
seta ♦ 1.2k • updated 13 months ago
Devon Ryan 90k
1
Vote
0
Replies
160
Views
Confused about read pair orientation in bam
alignment bam bwa paired end
13 months ago
malthesr • 10
0
Votes
3
Replies
171
Views
How to tell whether a bam file is "analysis-ready" (as defined by GATK)?
bam gatk bestpractice
14 months ago
minimax • 0
0
Votes
3
Replies
189
Views
scRNAseq: Split FASTQ into cell specific FASTQ Files
RNA-Seq Cell Ranger Split Demultiplex BAM
14 months ago
niklas.lang • 0
3
Votes
4
Replies
160
Views
Getting only Indels and no SNPs after variant calling variant calling using HaplotypeCaller
RNA-Seq BAM SNP GATK Variant Calling
14 months ago
Susmita Mandal • 40
0
Votes
1
Reply
124
Views
FastQC Failed to create archive: null
sequence qc bam java fastqc
14 months ago
jason.williams • 0
1
Vote
1
Reply
173
Views
Read TCGA BAM files into TEtranscripts tool (python) without downloading them?
TCGA bam linux RNA-seq
14 months ago
Gema Sanz • 70
5
Votes
2
Replies
188
Views
How does bedtools bamtobed calculate end position
bed bam bedtools
14 months ago
6timings • 0 • updated 14 months ago
John Marshall ♦ 1.5k
0
Votes
0
Replies
145
Views
View MAF file and the reference sequence in a genome viewer/annotator along with SAM/BAM?
SAM BAM MAF viewer
14 months ago
DanielC • 80
12
Votes
13
Replies
9.1k
Views
Comparing And Plotting Coverage Between Two Bam Files
bam coverage genome chromosome
8.1 years ago
Rubal7 • 760 • updated 14 months ago
john.e.major.jr • 0
1
Vote
2
Replies
164
Views
How to split both bam files and annotation files as per chromosome number?
split bam sam chr annotation
14 months ago
Glory Basumata • 140
0
Votes
1
Reply
230
Views
Extracting CIGAR string from a specific region of a read in a bam file using pysam?
pysam RNA-Seq BAM CIGAR
14 months ago
kiki4133 • 0
6
Votes
9
Replies
233
Views
How to separate chrY from a WGS vcf file?
tabix dantelabs wgs yfull bam
15 months ago
krt • 0
1
Vote
5
Replies
325
Views
SNP calling with SAMtools on multiple samples
SNP samtools vcf bam
15 months ago
madeira.ag • 0 • updated 15 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
8.0 years ago
Wjeck • 480 • updated 15 months ago
Biostar 20
1
Vote
4
Replies
266
Views
Filtering BAM file to include PE reads that did not map, even though their mate did
BAM samtools filter mapping read
15 months ago
nute11a • 0 • updated 15 months ago
Istvan Albert 87k
0
Votes
2
Replies
214
Views
How to get output with read counts and read count percentages from bam file?
read counts bam samtools picard
15 months ago
bayramliaziz • 0 • updated 15 months ago
WouterDeCoster 39k
5
Votes
10
Replies
309
Views
Subsampling one bamfile multiple times?
sequencing bam subsample
15 months ago
wjdgmlcjf • 0
3
Votes
7
Replies
265
Views
Bam file MC tag as integer
ValidateSamFile bam sam MC
15 months ago
chariko • 30
3
Votes
5
Replies
264
Views
How to find a variant in a particular position in a bam file only using samtools
bam sam samtools
15 months ago
tw617 • 30 • updated 15 months ago
swbarnes2 5.7k
4
Votes
2
Replies
231
Views
Convert 2 SE bam to PE bam (alignment BWA mem)
alignment bam bwa
16 months ago
mynameliuxiang • 0 • updated 15 months ago
zx8754 7.5k
0
Votes
4
Replies
353
Views
Bam header editing
bam header
16 months ago
Huynh Nguyen • 0 • updated 16 months ago
Istvan Albert 87k
0
Votes
2
Replies
171
Views
Read In Function for BAM file processing
Script BAM
16 months ago
Jonas.Koch • 0
3
Votes
7
Replies
277
Views
Extract coverage from each nucleotide position of a genome in a bam file
bam bed coverage
16 months ago
MAPK ♦ 1.4k
1
Vote
1
Reply
220
Views
How do get additional bam statistics
RNA-Seq alignment bam samtools
16 months ago
t-jim • 30
8
Votes
12
Replies
368
Views
How to report genomic intervals essentailly overlapping in all files?
bedtools bed bam
16 months ago
Vijay Lakhujani 4.1k
3
Votes
8
Replies
257
Views
Find common reads between two bam files
sequencing bam reads
16 months ago
yp19 • 20 • updated 16 months ago
Pierre Lindenbaum 120k
11
Votes
0
Replies
427
Views
Generating consensus sequence from bam file
bam fasta consensus Tutorial
16 months ago
finswimmer 11k • updated 16 months ago
WouterDeCoster 39k
1
Vote
2
Replies
336
Views
How treat a Bam file with mutiple read groups (RG)
next-gen BAM GATK picard read group
16 months ago
zamani_2012 • 0 • updated 16 months ago
Pierre Lindenbaum 120k
3
Votes
3
Replies
355
Views
RNA-Seq QC for aligned files (bam)
RNA-Seq bam qc
16 months ago
genomics Newbie • 20 • updated 16 months ago
Friederike 4.2k
1
Vote
2
Replies
226
Views
Might @PG headers affect downstream analyses, and how can I safely remove them from a BAM file?
bam @PG read groups
16 months ago
olikidrod • 0 • updated 16 months ago
h.mon 25k
17
Votes
28
Replies
554
Views
collapsing transcript expression to gene-level expression
FeatureCounts BAM RNA-Seq
16 months ago
F ♦ 3.4k
1
Vote
3
Replies
253
Views
Subsampling aligned SAM/BAM files for RNA-seq analysis
RNA-Seq subsampling downsampling SAM BAM
16 months ago
mohammedtoufiq91 • 40 • updated 16 months ago
WouterDeCoster 39k
4
Votes
4
Replies
239
Views
How to remove bam files that don't contain matching reads
bowtie2 samtools BAM
16 months ago
samlambrechts299 • 130 • updated 16 months ago
Pierre Lindenbaum 120k
2
Votes
5
Replies
247
Views
Should I remove duplicates?
BAM Duplicates next-gen
16 months ago
F ♦ 3.4k • updated 16 months ago
ATpoint 17k
1
Vote
6
Replies
207
Views
Seeing only "N's" in tablet genome viewer?
genome viewer bam
16 months ago
tuj92050 • 0
2
Votes
4
Replies
316
Views
Extracting a chromosome from an indexed bam file?
bam chromosome samtools
16 months ago
tuj92050 • 0
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