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zavolanlab / zarp

The Zavolab Automated RNA-seq Pipeline

Home Page:https://zavolanlab.github.io/zarp/

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ALFA strandedness issue

mkatsanto opened this issue · comments

commented

Describe the bug
The alfa directionalities seem to be the opposite of the options used here:

zarp/workflow/Snakefile

Line 30 in b8bd29e

"alfa": "fr-firststrand",

zarp/workflow/Snakefile

Line 25 in b8bd29e

"alfa": "fr-secondstrand",

according to the alfa annotation, it seems the SF should be the firststrand: https://github.com/biocompibens/ALFA/blob/5aa4a37e731db91746e15b61693f87962afa61f4/Galaxy_toolshed_repositories/alfa/ALFA.py#L458
and the
and the SR should be the secondstrand:
https://github.com/biocompibens/ALFA/blob/5aa4a37e731db91746e15b61693f87962afa61f4/Galaxy_toolshed_repositories/alfa/ALFA.py#L465

commented

Took a look at real data and the initial values lead to reasonable statistics. So will keep as is for now. Maybe in the future a good ci test for alfa (or a better alternative) could be developed.