number of .bam reads mapping to genes in gff format
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8.0 years ago
Floydian_slip ▴ 160

Hi,

I have a gff file containing a gene set and I also have a .bam file with read mappings to the genome. How can I get the number of reads that map to each gene (which as Start/Stop codon, CDS, intron specified in the gff file).

Any help will be greatly appreciated.

Thanks,
-n

mapping bams gff • 2.9k views
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8.0 years ago

You can use featureCounts, htseq-count, or Rsamtools with GenomicFeatures in R (you'd need to use the findOverlaps() function). featureCounts and htseq-count are probably the easier options.

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+1 for featureCounts speed.

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8.0 years ago
Bert Overduin ★ 3.7k

You can use the intersect sub-command of bedtools with the -c option.

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