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y9c / m5C-UBSseq

Ultrafast bisulfite
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issue for library type #3

Open ponyaaaa opened 2 months ago

ponyaaaa commented 2 months ago

I notice that in this pipeline, hisat-3n uses --directional-mapping for mapping,is that means the pipeline only suitable for forward_stranded library？

y9c commented 2 months ago

Hi @ponyaaaa,

The orientation of the reads is reversed automatically if they are reverse strand library. Could you update me with more information about the library type you would like to analyze?

ponyaaaa commented 2 months ago

Thank you for your prompt reply! I apologize for not paying close attention earlier. Is it the --auto-rc option in cutseq that performs the reverse library conversion? Also, if my library is unstranded, can i use this pipline for analysis?

y9c commented 1 month ago

Hi @ponyaaaa, mapping m5C modification using unstranded libraries is not accurate. I can try to apply this pipeline, but might need more adjustment.