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Old 09-15-2014, 01:48 AM   #1
nasobema
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Default htseq-count: how to use multiple features?

From the documentation I can only find how to select a certain type of feature for counting, like "exon" (default) or "ncRNA".

Is there also a way to select multiple features?
I'm using it currently for bacterial transcriptomics and ncRNA are of increasing importance here. Currently, I still need to run the script twice on different features and merge the results afterwards.

While this actually works fine, it would be simpler to just tell htseq-count to look for multiple features at the same time.

Any hints on how to do this?
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Old 09-15-2014, 01:55 AM   #2
dpryan
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There isn't, but it would be simple to just modify the annotation file that you're using to just collapse exon and ncRNA into a single feature. Something like the following would work:

Code:
awk '{if($3 == "exon" || $3 == "ncRNA") {$3="interesting_feature"}; print $0}' foo.gtf > foo.modified.gtf
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Old 09-15-2014, 02:33 AM   #3
nasobema
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Quote:
Originally Posted by dpryan View Post
There isn't, but it would be simple to just modify the annotation file that you're using to just collapse exon and ncRNA into a single feature. Something like the following would work:

Code:
awk '{if($3 == "exon" || $3 == "ncRNA") {$3="interesting_feature"}; print $0}' foo.gtf > foo.modified.gtf
OK, sure. But then, there wouldn't be the option to separate the feature types any more. Unless I maintain multiple annotation files, of course.

Seems like I have to stick to workarounds.
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Old 09-15-2014, 02:37 AM   #4
dpryan
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A work around might prove simpler, yes. featureCounts also doesn't seem to support this, though I suppose you could just alter the source code for either of them to add this functionality.
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