Hi! I used cutadapt on my PE reads, and then FASTX to collapse duplicate reads in my data. Then I proceeded to do bowtie2 - turns out that there was a different no. of reads in R1 than R2 so bowtie could not run at all! I assume this was not do to FASTX, but rather to cutadapt (I specified to remove reads that became too short after trimming). so my questions are:
- Am I right in my assumption regarding cutadapt?
- Is there any way to make the reads appear even again, without hurting the data? (I was not sure if just adding reads would be OK or not).
Thanks for the help!