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Update README.md
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Ingefast authored Nov 10, 2022
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Expand Up @@ -71,8 +71,6 @@ working_dir="/media/diskb/nicolas_tmp/REPLICATES_TOTAL"
#this defines the samples to be analysed (dir names)
sample_list="mutant_rep1 mutant_rep2 wt_rep1 wt_rep2";
#sample_list="test_rep1";
```
If removing structural RNAs is wanted before downstream processing, a fasta file with the selected structural RNAs (including e.g. pre-tRNA, snoRNA, snRNA, rRNA) has to be prepared (with e.g. bedtools getfasta) and bowtie-indexed accordingly. Otherwise the pipeline can easily be modified skipping this step.

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