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bam-readcount -p option

By reading the documentation I get the impression that the -p switch is for running bam-readcount on multiple libraries in one go, i.e. multiple BAM files. However, I can't really figure out whether I'm supposed to supply a list of files or do something else, and I can't find any example of its usage.

Does anybody have any idea?

bam-readcount
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updated by Ram Ram • written by philip.jonsson • philip.jonsson

Not sure if per library handled multiple BAM files. Could just be multiple libraries from a single BAM file, in which case you might need to merge BAMs

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written by Ram Ram

Ah, of course. That hadn't occurred to me but makes sense.

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updated by Ram Ram • written by philip.jonsson • philip.jonsson

I'm not sure though - just something that seems plausible given the usage format in the documentation.

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written by Ram Ram

1 answer

What RamRS says is true, the program is designed to run on a single BAM file only. The -p flag enables reporting by library for all libraries in a single BAM file. If you have any suggestions on how to make the documentation clearer, please let me know.

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updated by Ram Ram • written by ernfrid ernfrid

There's just a small window open for misinterpretation, and I happened to look through that window. Not sure any change is needed, but if you were to change anything I guess it would be to more explicitly state that multiple libraries in one BAM file can be analyzed.

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updated by Ram Ram • written by philip.jonsson • philip.jonsson

<bamfile> usually means a single input. Multiple inputs are usually designated with one mandatory and then a few optional, like so:

<bamfile1> [[bamfile2] [bamfile3] ... [bamfileN]]
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written by Ram Ram

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