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Question: Counting ambiguously mapped reads per feature
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gravatar for rubi
2.2 years ago by
rubi90
rubi90 wrote:

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?

 

ADD COMMENTlink modified 2.2 years ago by Gordon Smyth35k • written 2.2 years ago by rubi90
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gravatar for Gordon Smyth
2.2 years ago by
Gordon Smyth35k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth35k wrote:

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

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Gordon Smyth35k
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gravatar for Steve Lianoglou
2.2 years ago by
Denali
Steve Lianoglou12k wrote:

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 COMMENTlink written 2.2 years ago by Steve Lianoglou12k
2

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 REPLYlink written 2.2 years ago by Michael Love19k
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