Per Base Coverage
Is there a way to obtain per-base coverage for a define chromosome interval using a bam file generated from Illumina single-end reads? genomeCoverageBed in Bedtools does not seem to have an option for it.
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Aaronquinlan
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written
by
Info_Nowise •
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written
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Info_Nowise •
2 answers
samtools depth your.bam
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link
updated
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Ram
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written
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Zev.Kronenberg
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written
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Zev.Kronenberg
Also,
bedtools coverage -abam aln.bam -b regions.bed -d
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link
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Ram
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written
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Aaronquinlan
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written
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Aaronquinlan
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