Low mapping ratio and lost reads after realigngap and filter about pseudou-bidseq

[y9c]

Thank you @erhei01. Low mapping ratio might caused by improperly adapter trimming. Could you show me which dataset you have tested and the adapter in your settings?

[erhei01]

Thanks for your reply.
I ran your Snakefile with default settings on SRR15082607~SRR15082610 of GSE179798 and I found the deduping and mapping records in workspace/report_reads directory.

[y9c]

The default settings of this repo do not fit the data you mentioned. This method is quite different from the previous paper. If you want to reproduce the results, I would recommend you to follow the method described in the paper.

This method can be adapted to the previous data by adding barcode: NNNNNXXX-XXXNNNNNATCACG in the yaml file, but the result is not guaranteed to be exactly the same. If you use the default settings, the inline barcode won't be trimmed and lead to low mapping ratio.

If you have any questions or suggestions, feel free to open new issues.