Open ponyaaaa opened 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?
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?
Hi @ponyaaaa, mapping m5C modification using unstranded libraries is not accurate. I can try to apply this pipeline, but might need more adjustment.
I notice that in this pipeline, hisat-3n uses --directional-mapping for mapping,is that means the pipeline only suitable for forward_stranded library?