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Is there a way to save the duplicates (write to a separate file) that are removed by SAMtools' rmdup? I'd like to have a look at them....
Many thanks in advance,
K
Many thanks in advance,
K
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try picard MarkDuplicates and then using samtools view -f 1024 -
Cheers, that makes sense. I wish there was a way of doing this in a single step with samtools (I'm not so fond of Picard at the moment...
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KComment
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Is it too obtuse to say that you could grep out the non-matching lines from the rmdup SAM and the original SAM?
Also whats wrong with Picard? I've always found it more consistent.Comment
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Picard MarkDuplicates doesn't work with SE reads, as far as I can tell.
We're estimating duplicates in ChIP-seq data.Comment
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i am not sure of this. why wouldnt it?Originally posted by robinpsmith View Post
anyway, depending on your alignment file size you could also consider running a unix diff on the original and samtools-rmdup'ed SAM file.Comment
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Hi,
Am using samtools rmdup ... but it doesn't seem to remove them in the out file? What's going on?
NashComment
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@volks you are right, it does work on SE. My bad.
@naragam. I ended up using Picard, it does a much better job.Comment
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