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1
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Getting all the genomic coordinates where RNA-seq reads are split within a given genomic interval in a bam file
reads cigar splicing bam rna-seq written 2 days ago by rubic • 200 • updated 2 days ago by Pierre Lindenbaum ♦ 133k
4
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1
answer
107
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1
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How to check size of genome?
bam bp written 4 days ago by arianc • 0 • updated 3 days ago by Alex Reynolds ♦ 31k
3
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1
answer
109
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1
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How to convert fastq to bam?
fastq bam written 10 days ago by arianc • 0 • updated 10 days ago by ATpoint ♦ 44k
1
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1
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70
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1
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Combine multiple samtools view
alignment samtools bam written 10 days ago by rah • 20 • updated 10 days ago by GenoMax ♦ 94k
0
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0
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97
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0
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Formatting BAM file and GTF file for feature counts
alignment featurecounts rna-seq bam written 20 days ago by abhilashtripathi10 • 0
3
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1
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2.4k
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1
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Program to calculate and add the NM tag to a bam file
nm bam written 3.5 years ago by abascalfederico • 1.1k • updated 20 days ago by Biostar ♦♦ 20
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0
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111
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0
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How to create coverage graph/plot for an entire Illumina run
R bam coverage graph plot written 24 days ago by SaltedPork • 110
2
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1
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158
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1
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Soft Clipped read 3' end position
htsjdk java bam written 24 days ago by mhasa006 • 50 • updated 24 days ago by d-cameron • 2.3k
0
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1
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127
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1
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paired-end bam clip bases outside insert range
bam short insert size trimming by coordinate written 26 days ago by pau.rodriguez.sodupe • 10 • updated 25 days ago by Pierre Lindenbaum ♦ 133k
0
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0
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88
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Multisample BAM file
snp calling bam samtools written 25 days ago by gubrins • 60 • updated 25 days ago by vareenjuriya • 0
12
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3
answers
2.6k
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3
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Make bam index human readable
bai bam index written 5.0 years ago by dariober ♦ 11k • updated 27 days ago by baye.james • 10
1
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0
answers
138
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0
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How to calculate VAF from BAM or SAM(+pileups) files using pysam?
bam vaf pysam snp sequencing written 27 days ago by askif4 • 0
0
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0
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129
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0
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help with calling invariant sites in parallel: scaffolds not present in all bam files are skipped
invariant bam bcftools scaffold written 4 weeks ago by truebeliever24 • 20
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1
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122
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1
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Problem with qualimap BAM file
qualimap bam bamfile error rna-seq written 4 weeks ago by luzglongoria • 40 • updated 4 weeks ago by Pierre Lindenbaum ♦ 133k
0
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0
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123
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0
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Extract aligned reads from a bam file for only selected coordinates
alignment samtools pacbio bam written 5 weeks ago by star715 • 20
1
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1
answer
122
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1
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Extracting only reads mapped to specific genomic region
fasta bam mapping written 6 weeks ago by agata • 10 • updated 6 weeks ago by JC ♦ 12k
0
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1
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142
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1
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What exactly does the -fs flag (fragment size) do in bedtools genomecov/genomeCoverageBed?
bedtools bed bam read mapping written 6 weeks ago by kieft1bp • 0 • updated 6 weeks ago by ATpoint ♦ 44k
3
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1
answer
181
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5 follow
1
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How to count the number of alignments in a bam file without using samtools?
bam written 6 weeks ago by steve • 2.7k • updated 6 weeks ago by xiaoguang • 50
1
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0
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139
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0
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Tool: Filtering BAM files efficiently
genome alignment sam bam tool written 6 weeks ago by ddeemer • 0
5
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1
answer
2.5k
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7 follow
1
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Tutorial: bam2rpkm by bedtools
bedtools rpkm tutorial bam rna-seq written 3.2 years ago by jmzeng1314 • 110 • updated 6 weeks ago by ATpoint ♦ 44k
1
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0
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120
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0
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Variant Calling - Ion Torrent
variant calling iontorrent bam written 7 weeks ago by AndreaSibi • 0
90
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7
answers
61k
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58 follow
7
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How to plot coverage and depth statistics of a bam file
sequencing next-gen coverage bam depth written 6.6 years ago by krithika.gu • 280 • updated 7 weeks ago by Pierre Lindenbaum ♦ 133k
8
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1
answer
221
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1
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genome coverage visualization
genome bedtools bam coverage written 7 weeks ago by gubrins • 60 • updated 7 weeks ago by bernatgel • 2.8k
4
votes
1
answer
180
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1
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How to annotate a bam file?
bam annotations written 8 weeks ago by Assa Yeroslaviz • 1.4k
1
vote
1
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246
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1
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Read name not stored in CRAM file. Is it possible to create new read names for remapping?
cram bam samtools sequencing written 9 weeks ago by cl • 0 • updated 8 weeks ago by jkbonfield • 470
10
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3
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208
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3
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Split paired end fastq per lane from a bam file
fastq bam written 10 weeks ago by MAPK • 1.7k
0
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0
answers
132
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0
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Star RNA seq aligner issue:
bam star rna-seq written 9 weeks ago by play.tatha • 0
0
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1
answer
130
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1
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Transcript sequence aligns twice on the reference
alignement bam written 10 weeks ago by pablo • 150 • updated 10 weeks ago by JC ♦ 12k
1
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0
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171
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0
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Two bams with similar flagstat output have very different file size
flagstat alignment bwa bam written 10 weeks ago by freeheart.steven • 10 • updated 10 weeks ago by a.alnawfal.1992 • 110
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1
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5.6k
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7 follow
1
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Truncated sam file - Parse error
bam sam bwa written 3.4 years ago by fiona.newberry • 80 • updated 10 weeks ago by dB • 0
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