Open JustGitting opened 9 years ago
It seems that the "-Q 20" did not work as expected. Could you run it again without the parameter "-f sanger"?
Hi Relipmoc,
So I re-run skewer without the "-f sanger" option and there was a major improvement.
$ zgrep NNNNNNNNNNNNNNNNNNNNNNNNN S1_L001_001_skewer-trimmed-pair1.fastq.gz | wc -l
26
The fastqc per-base quality looks better too.
What's the next step?
Hi,
I'm just trying out skewer on some 2 x 150bp Nextera Mate pair reads (sequenced on a NextSeq) from a endophyte (fungus), so forgive me if I've setting something wrong.
In one of the raw read files, I found a large number of N sequences.
So using mostly default settings, I ran skewer as follows:
Checking the log we have:
However, the resulting trimmed file still contains large numbers of NNNN's.
I've check the documentation and it's no clear as to why there are large runs of N's.
Further, running Fastqc (v 0.11.3) shows there is virtually no difference between the "per base sequence quality" of the raw reads and the trimmed reads (-Q 20), as seen in the raw graph:
Skewer per base quality graph:
Any advice much appreciated.