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From raw illumina reads data to counts
Need to redirect standard output to record in a log file. Follow previous scripts format to do this.
Trimmomatic and cutadapt do not trim reverse complements of adapters. Add revcomp to the github univec and provide warning in README.
Currently bowtie2 output details (alignment statistics) are only writing to screen. These should be captured and put in a log file. Specifically 01_scripts/02_bowtie2_aln*
scripts.
There are old components of the readme that are no longer used, and there are sections that need to be updated.
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