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<prev • 1,077 results • page 1 of 36 • next >
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How to split BAM files by samples from PacBio
bax bam pacbio written 4 hours ago by bwczech • 0
4
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2
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79
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6 follow
2
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How to extract the same mapped region by multiple samples ?
samples bam map written 1 day ago by Picasa • 390 • updated 1 day ago by Alex Reynolds ♦ 26k
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2
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109
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Is there a tool or method for phasing a VCF based on an already phased BAM?
vcf haplotype phasing bam written 6 days ago by olavur • 70
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2
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116
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How would you filter PCR duplicates for merged paired-end reads
alignment bam pcr duplicate written 8 days ago by hohoku • 0
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2
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107
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2
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find coverage of specific exomes from a bam file
bedtools genomecov bam coverage bed written 5 days ago by lait • 120 • updated 5 days ago by Pierre Lindenbaum ♦ 114k
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1
answer
177
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1
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Get sequences from a BAM file as strings spaced out as described by cigar
R alignment genomicalignments bam cigar written 7 days ago by yesitsjess • 0 • updated 7 days ago by Matt Shirley ♦ 8.7k
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1
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106
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5 follow
1
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Making a counts
feauturecounts bam counts rna-seq written 8 days ago by frozmanik • 0 • updated 8 days ago by h.mon ♦ 21k
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5
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10 follow
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What Is The Fastest Method To Determine The Number Of Positions In A Bam File With >N Coverage?
bedtools depth-of-coverage bam samtools coverage written 5.5 years ago by Malachi Griffith ♦ 16k • updated 13 days ago by Paul • 1.2k
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127
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1
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Get genes and coverage/depth per gene from sam/bam
ngs bam sam coverage per gene depth per gene written 13 days ago by prishly • 0 • updated 13 days ago by Charles Warden ♦ 5.6k
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1
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129
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1
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Converting mapped + unmapped BAM files to raw FASTQ (RNA-seq data)
bam2fastq bam fastq conversion rna-seq written 14 days ago by rodd • 20 • updated 14 days ago by swbarnes2 ♦ 4.5k
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103
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1
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BAM file doesn't show the altered sample identifier
fastq bam written 14 days ago by Badh2 • 0 • updated 14 days ago by finswimmer ♦ 6.7k
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101
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Extracting specific regions from a bam file and exporting them to do a phylogenetic analysis
phylogenetic fasta bam samtools geneious written 15 days ago by Badh2 • 0
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Adding read groups to large BAM files
alignment bam written 15 days ago by Fungsten • 0 • updated 15 days ago by ATpoint ♦ 9.1k
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6
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20k
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16 follow
6
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Where Can I Download Some Bam Files?
bioinformatics bam rna-seq written 6.5 years ago by snakesgun • 110 • updated 15 days ago by Roman Valls Guimerà • 510
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3
answers
103
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3
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How to extract coordinate of hard and soft clipped long reads ?
clipped longreads mapping bam written 19 days ago by BioGeek • 130 • updated 19 days ago by Carambakaracho • 570
3
votes
1
answer
118
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1
answer
How to annotate chloroplast genome
.gff annotation bam written 19 days ago by kristina.mahan • 20 • updated 19 days ago by goodez • 380
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127
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Using samtools to assess the number of reads that cover a variant position, as well as the ratio of ref/alt among those reads
allele balance bam samtools rna-seq mpileup written 19 days ago by claudiadast • 0
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5
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1.9k
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11 follow
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Download SAM/BAM files from SRA takes ages!!!
sra bam written 15 months ago by Alejandro Jimenez Sanchez • 120 • updated 20 days ago by shengwei • 30
17
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0
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555
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Tool: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
bam sam sort markduplicates bqsr tool written 22 days ago by Charlotte.Herzeel • 110 • updated 21 days ago by Leonor Palmeira ♦ 3.6k
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184
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2
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Is there a single header file somewhere I can use to read bam?
bam C c++ written 22 days ago by Click downvote • 650 • updated 22 days ago by John Marshall • 1.4k
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2
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233
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2
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Reheadering a subsetted bam gives truncated file
reheader header samtools bam written 3 months ago by Luciferine • 0 • updated 25 days ago by Biostar ♦♦ 20
1
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1
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1.4k
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1
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Varscan2 copynumber 'Parsing Exception' error
varscan2 copynumber samtools bam whole exome written 2.2 years ago by Vanish007 • 10 • updated 27 days ago by jgarces • 0
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3
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8 follow
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Extracting Read Pairs From Region So That All Pairs Remain Intact
fastq picard samtools bam written 5.2 years ago by Davy • 360 • updated 28 days ago by cmdcolin • 920
2
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1
answer
140
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1
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Can anyone point me in the direction of some raw BAM formatted bacterial PacBio data
metagenomics bam prokaryotes pacbio pbccs written 4 weeks ago by TEF • 0 • updated 4 weeks ago by genomax ♦ 58k
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1
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196
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5 follow
1
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loaded a sorted bam file in IGV but I can't see anything
assembly bam igv written 5 weeks ago by saadleeshehreen • 40 • updated 5 weeks ago by Emily_Ensembl ♦ 16k
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125
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what is the easiest/fastest way to convert from BAM to GTF
gtf bam written 5 weeks ago by Sam • 80
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120
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Reads that map to two different genomes, but with different map coordinates
ngs bam bamutil comparison bamutil diff written 6 weeks ago by Susmita Mandal • 0
0
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1
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114
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1
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Multi-part TCGA BAMs?
data bam cancer written 6 weeks ago by lucas.lochovsky • 0 • updated 6 weeks ago by Kevin Blighe ♦ 31k
6
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1
answer
184
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1
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unsuccessful split of bam file by samtools and bamtools
samtool split bam bam bamtoo written 6 weeks ago by grobelsek.v • 0
1
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345
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Adding read group to bam files from multiplexed samples
gatk picard bam written 3 months ago by serpalma.v • 20 • updated 6 weeks ago by Biostar ♦♦ 20
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