How to count different features at the same time with htseq

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6.3 years ago

Javad ▴ 150

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 • 1.6k views

ADD COMMENT • link 6.3 years ago by Javad ▴ 150

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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 REPLY • link 6.3 years ago by ATpoint 85k

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Then how the command would look like?

ADD REPLY • link 6.3 years ago by Javad ▴ 150

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

ADD REPLY • link 6.3 years ago by ATpoint 85k

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