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Old 09-30-2015, 11:47 AM   #1
Location: St. Louis

Join Date: Jan 2012
Posts: 15
Default Mate Pair QC

I've been using a combo of fastqc and cutadapt to qc some mate pair libraries we have.

This is a Truseq LT matepair library

I'm only interested in pairs that have evidence of the junction adapter.

cutadapt -m 50 -B CTGTCTCTTATACACATCT -B AGATGTGTATAAGAGACAG -b CTGTCTCTTATACACATCT -b AGATGTGTATAAGAGACAG --trimmed-only -o r1.fastq -p r2.fastq A2YH4_R1.fastq  A2YH4_R2.fastq
This made two separate files that had the junction removed... perfect.

Now when I run fastqc, I expected to see some adapter to match (because I removed the junctions first).

I was surprised instead to see such a high kmer bias, none of the kmers seem to quite match an illumina adapter.

The question is, what explains this kmer bias? Should I just trim the first 45 bases? Is it because I'm dealing with a repetitive plant genome?
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Old 09-30-2015, 01:11 PM   #2
Location: St. Louis

Join Date: Jan 2012
Posts: 15

Looks like some cloning vector snuck in. fastqc didn't put it into the overrepresented sequences table, but that seems to be the problem, now to figure out what it is doing there.

I figured it out by doing a simple grep of the kmer, then my eyeballs saw there was more adapter there. Blasting confirmed it was a cloning vector.
cwisch88 is offline   Reply With Quote

assembly, fastqc, mate pair, trimming, truseq

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