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Old 02-18-2020, 07:55 AM   #1
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Default How to properly concatenate reads from PE sequencing files for alignment

I have PE RNA-seq fastqs and I get 65-75% uniquely mapped reads using STAR. I wanted to merge across samples so I concatenated into separate R1 and R2 files for each group. When I align the merged files with STAR, it gives me almost no uniquely mapped reads. The log file says that the % of unmapped reads is around 98-99% due to being too short.

Does anyone know why these won't map? Is there a better way to do this? I've looked at other threads and the approach I used is similar, i.e., simply using cat to concatenate them in order. But nothing gives a reason why they might not be mapping.
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