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novoalab / EpiNano

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
GNU General Public License v2.0
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output of sam2tsv not parsed correctly, perhaps? #76

Closed EmanueleRaineri closed 3 years ago

EmanueleRaineri commented 3 years ago

Hi,

thanks for your work on Epinano.

Not sure if it's a mistake on my side, but I seem to be getting incorrect chromosome names in the output of Epinano_Variants.py.

I think you assume that the output header of sam2tsv is #READ_NAME FLAG CHROM READ_POS BASE QUAL REF_POS REF OP STRAND

whereas the real header is

#Read-Name Flag MAPQ CHROM READ-POS etc...

and so MAPQ is used instead of CHROM in the subsequent parsing?

but I'm not sure if this is the problem, or if there's something else.

Huanle commented 3 years ago

Hi @EmanueleRaineri ,

Probably you are using a different version of sam2tsv than the one used by epinano. Can you try with misc/sam2tsv.jar ?

EmanueleRaineri commented 3 years ago

Makes sense. I didn't notice you were redistributing sam2tsv and installed a fresh copy. misc/sam2tsv has a different header, which i assume matches your code. At the moment I modified my local version of EpiNano so that it works with the sam2tsv I installed, but I will let you know if I roll back my changes to test with misc/sam2tsv. Thanks for your reply.