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Old 02-06-2014, 11:13 PM   #5
Location: Los Angeles, CA

Join Date: Jul 2011
Posts: 58

It seems that the adapter sequences had not been trimmed for some paired-end reads.

Possible causes:
1. Adapter sequences (one for read1 and the other for read2) were not specified properly;
2. The sequencing error rate is significantly higher than expected (e=0.1 by default), especially in the 3' end regions of the reads.

1. Double check whether the adapter sequences were specified correctly;
2. Use a higher expected error rate (e.g. -e 0.25).

BTW: I also suggest you try skewer for this task since it's dedicated to trimming adapters in paired-end reads.

Originally Posted by wonaya View Post
I need help in interpreting the fastQC results I have on my sample from paired-end ChIP-seq (151bp long from miseq)

After removing adapter sequences using trim-galore, I am still seeing strange kmer patterns at the 3' end of reverse reads. Does anyone know where these might have originated from, or is it possibly some parameters I've not used in trim-galore?

trim_galore --fastqc -a *adapter_sequence* --paired read_1.fastq read_2.fastq

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