Mapped Read Counts For Rna-Seq Analysisusing Samtools In R

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10.3 years ago

robjohn7000 ▴ 110

Hi,

Is it possible to use samtools, just as HTSeq count, count the mapped reads for RNA-Seq analysis? This is not clear in the documentation.

Thanks

rna-seq r • 3.0k views

ADD COMMENT • link 10.3 years ago by robjohn7000 ▴ 110

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No, it's not possible. You could probably hack together a solution (using a BED file as the annotation), but that'd be a waste of time given that there are already tools to do that.

Edit: It's unclear what any of this has to do with R. There's an Rsamtools package, which I have to admit I've never found very useful, but you could use to do counting in combination with other packages (I think there's an example in the GenomicFeatures or GenomicRanges packages).

ADD REPLY • link 10.3 years ago by Devon Ryan 104k

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I don't think so. at best, you can compute the coverage with the mpileup command. HTSeq-count is usually used for this task, is there a reason why you don't want to use it?

ADD REPLY • link 10.3 years ago by Martombo ★ 3.1k

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Thanks for your comments everyone. I have had problems in the past with gff which is required by HTSeq-count, so I was just looking for alternative tools.

ADD REPLY • link 10.3 years ago by robjohn7000 ▴ 110

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