Question: How to count different features at the same time with htseq
gravatar for Javad
20 months ago by
Javad90 wrote:

Dear all,

I want to do counting of my data set and I do like to count the number of reads aligned to the gene, UTR and sRNA at the same time. As the --type argument of htseq only accepts one feature at a time, is there a way that I can count these features together.

And if this is not possible with htseq, which other software do you suggest to perform this type of counting.

Thanks a lot in advance, Best

rna-seq • 523 views
ADD COMMENTlink written 20 months ago by Javad90

Not sure about htseq, but featureCounts (subread package) accepts a custom annotation format (SAF, check their manual). You could make a custom reference, including all the features you want, and then simply quantify against that.

ADD REPLYlink modified 20 months ago • written 20 months ago by ATpoint31k

Then how the command would look like?

ADD REPLYlink written 20 months ago by Javad90

Tried anything yet? Spoon-feeding will not help you improve yourself.

ADD REPLYlink written 20 months ago by ATpoint31k
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