User: vitor.rca

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Posts by vitor.rca

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Comment: C: Sort BAM files by reference, and then by read name within each reference?
... OK, thank you. It takes a long time to split a BAM with `bamtools split`, I mean, more time than I was anticipating for a BAM already sorted by position. So I was hoping for an alternative, but it seems like there's no reason for someone to implement such sorting scheme, since no tool requires it, e ...
written 15 days ago by vitor.rca0
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Comment: C: Sort BAM files by reference, and then by read name within each reference?
... The default behavior of samtools sort does that: "When the -n option is not present, reads are sorted by reference (according to the order of the @SQ header records), then by position in the reference". I am asking how to sort by reference, then by read name. ...
written 15 days ago by vitor.rca0
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Sort BAM files by reference, and then by read name within each reference?
... Is there an efficient way to sort a BAM file by chromosome, and then by read names within each chromosome? I could split the BAM by chromosome, sort each resulting BAM by read names, and finally merge the list of BAMs. But I wonder if there is a single and straightforward command to do that. ...
alignment rna-seq written 15 days ago by vitor.rca0 • updated 15 days ago by Pierre Lindenbaum133k

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