How to count different features at the same time with htseq
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
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Not sure about
htseq, butfeatureCounts(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.Then how the command would look like?
Tried anything yet? Spoon-feeding will not help you improve yourself.