Hi guys,
I recently encountered some RNAseq data with extremely high adapter content (over 90% of reads with about 50% adapter contents) and low alignment rate (<2%, GRCH38).
Are these reads contamination (not from human)? Should I discard the reads with high adapter contents? Is there a way to rescue these data?
The pic shows the alignment after trimming adapters using trimgalore with default settings.
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They don't look like adapters. They are 50bp long. I trimmed them then the reads are too short to align.
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