Hello,
we've done a RNA-Seq analysis (Illumina HiSeq2000, 50 bp, paired end) and I have checked the quality with FastQC. There raised some questions for me:
1. Is FastQC as quality check alright for paired end reads?
2. The program gives for all of my four samples a fail for the per base quality of the second read (only the last three bases show lower quartile less than 5 or a median less than 20). Is there a logical explanation?
3. The sequencing and mapping was done by a company and they told us they trimmed the adapters. But I get a fail in the dublication level and if you look at the overrepresented sequences I can see only primer or adapter sequences. Did they a bad job?
Thanks for your help! Isabelle
we've done a RNA-Seq analysis (Illumina HiSeq2000, 50 bp, paired end) and I have checked the quality with FastQC. There raised some questions for me:
1. Is FastQC as quality check alright for paired end reads?
2. The program gives for all of my four samples a fail for the per base quality of the second read (only the last three bases show lower quartile less than 5 or a median less than 20). Is there a logical explanation?
3. The sequencing and mapping was done by a company and they told us they trimmed the adapters. But I get a fail in the dublication level and if you look at the overrepresented sequences I can see only primer or adapter sequences. Did they a bad job?
Thanks for your help! Isabelle
Comment