I'm using RNAseq for DGE and failed in trying to map paired end reads in TopHat2. Samples passed the first two parts of fastqc, but failed per base and Kmer count. Some samples did pass per base.
I tried trimming them to remove adaptors, but nothing improved the Kmer plot. http://imgur.com/Fhbx534 All of the kmer plots from this data set (18) look similar. I used the adaptor settings built into trimmomatic, but none worked. I then emailed genewhiz and asked for their (truseq) adaptors, but trimming for those sequences didn't improve the plots.
Ex per seq quality score http://imgur.com/5L5PaJU,Hg2mHk0#0
per base http://imgur.com/5L5PaJU,Hg2mHk0#1
Am I doing something wrong? Should I just trim everything across certain bases?
Edit: reads are paired
adaptor input file:
>PrefixPE
GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
>Prefix PE
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
I tried trimming them to remove adaptors, but nothing improved the Kmer plot. http://imgur.com/Fhbx534 All of the kmer plots from this data set (18) look similar. I used the adaptor settings built into trimmomatic, but none worked. I then emailed genewhiz and asked for their (truseq) adaptors, but trimming for those sequences didn't improve the plots.
Ex per seq quality score http://imgur.com/5L5PaJU,Hg2mHk0#0
per base http://imgur.com/5L5PaJU,Hg2mHk0#1
Am I doing something wrong? Should I just trim everything across certain bases?
Edit: reads are paired
adaptor input file:
>PrefixPE
GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
>Prefix PE
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Comment