todo.txt

- cuffdbs change dramatically in size if gtf is provided when building them, but what impact does it have on the results

- Also try to remove RNA PCR Primer enrichment. Currently we just remove index and universal adapter


1) evaluate if trimmoatic is the better trimmer (with respect to cutadapt)
- also consider to use contamination list from fastqc for trimming (see https://www.biostars.org/p/15753/)


Multi-Mapper
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- perl filter does not seem change tophat results
- samtools view -bq1 removes something (nur bei tophat default "-g 20")
- "-g1" --> no multimapper in algn_summary and not filter effect


next:
- are removed/remaining counts consistent with reported multimapper counts from algn_summary.txt
- are there duplicated read ids when using -g1