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Question: featureCounts for multiple features
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gravatar for hwu12
11 weeks ago by
hwu1210
hwu1210 wrote:

Hi, I am using the linux version of featureCounts, and I would like to count the number of reads in CDS, 5'UTR and 3'UTR. I was wondering if I should just count three times like:

featureCounts -t CDS -g gene_id -a $GTF -o counts.txt $BAM

featureCounts -t five_prime_UTR -g gene_id -a $GTF -o counts.txt $BAM

featureCounts -t three_prime_UTR -g gene_id -a $GTF -o counts.txt $BAM

Or is there a way to do all three together? Thanks!!!

 

 

 

 

ADD COMMENTlink modified 10 weeks ago by Wei Shi2.9k • written 11 weeks ago by hwu1210
3
gravatar for Wei Shi
10 weeks ago by
Wei Shi2.9k
Australia
Wei Shi2.9k wrote:

Regarding questions related to featureCounts that is released as part of the SourceForge Subread package, please send your question to Google Subread group (https://groups.google.com/forum/#!forum/subread).

You cannot count reads to three different types of features at one time with your current GTF annotation file. However you can get around this by changing the names of the three feature types to the same name, for example you may rename all of them to 'CDS_or_5UTR_or_3UTR'. Then you can count reads to all the three types in one command:

featureCounts -t CDS_or_5UTR_or_3UTR -g gene_id -a $GTF -o counts.txt $BAM

But this might take more effort than simply summing up the counts you got from the three individual counting.

ADD COMMENTlink modified 10 weeks ago by Gordon Smyth35k • written 10 weeks ago by Wei Shi2.9k

Thanks so much, Wei and Gordon!!!

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by hwu1210
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