Question

Counting ambiguously mapped reads per feature

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rubi ▴ 110

@rubi-6462

Last seen 5.7 years ago

Hi,

I have a bam file in which ~50% of the reads map ambiguously (since the library is from small RNAs). For each feature (e.g., gene) in my GTF file I'd like to add a count of 1 if a read from that bam file maps to that feature uniquely and 1/n if a read maps to n locations (that feature being one of them).

Is there any Bioconductor code that can achieve that?

rnaseq bam genomicranges GenomicAlignments Rsamtools • 1.4k views

ADD COMMENT • link updated 7.8 years ago by Gordon Smyth 50k • written 7.8 years ago by rubi ▴ 110

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Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 14 months ago

United States

You might try using tools like salmon, kallisto, or RSEM, which provide a more principled (and community-vetted) approach to solving this exact issue.

ADD COMMENT • link 7.8 years ago Steve Lianoglou ★ 13k

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Here are my Bioc2016 slides on using these quantifiers with Bioconductor software packages:

http://mikelove.github.io/bioc2016

In particular, see slide 4 for an idea how you can do better than assigning 1/n to all of the potential alignment locations.

ADD REPLY • link 7.8 years ago Michael Love 41k

score 3 · Accepted Answer · 2016-07-22

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Gordon Smyth 50k

@gordon-smyth

Last seen 1 hour ago

WEHI, Melbourne, Australia

Rsubread::featureCounts() with countMultiMappingReads=TRUE and fraction=TRUE does exactly that.

ADD COMMENT • link 7.8 years ago Gordon Smyth 50k