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Old 10-24-2013, 10:21 AM   #5
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Location: USA

Join Date: Oct 2013
Posts: 2

FASTQC on my small RNA sequences identifies several overrepresented sequences. It might be because of the adapter sequences. I do a trimming for the adapter ('ACTA') using the command
>fastx_clipper -C -v -i SRR519779.fastq -Q 33 -a ACTA -o SRR519779_trimmed.fastq
The out put for this is:
Clipping Adapter: ACTA Min. Length: 5 Clipped reads - discarded. Input: 4484151 reads. Output: 4440775 reads. discarded 0 too-short reads. discarded 0 adapter-only reads. discarded 0 clipped reads. discarded 43376 N reads.

Seems there is no effect of this trimming, the FASTQC shows similar results on the trimmed sequence.
Am I doing something wrong? Please suggest.
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