BIOPZ-Katsantoni Maria authored 4 years ago and Alex Kanitz committed 4 years ago

In labkey_to_snakemake.py fixed the parameters so that there is 3p as well 5p polya
feature for every mate, which can be matched to the -a -g -A and -G options of cutadapt
depending on which is the sense or antisense mate the appropriate variable is populated
and the rest of variables are filled with 'XXXXXXXXXXXX' which leads to no trimming by
cutadapt. The poly-A trimming rules are fixed to contain all -a -g -A -G options.

Dominik Burri authored 5 years ago and CJHerrmann committed 5 years ago

fixed typos

updated pipeline documentation

described seqmode specific rules

adapted to updates in Snakefile

moved star_rpm and samtools index to main snakefile description

linked README in documentation and vice versa