Hi,
I am trying to do some DE-analysis with different TruSeq paired-end samples. As I'm new to RNA-Seq I'd like to ask for some advice/opinions on my data and my quality control settings.
I use fastqc for quality control and none of my samples look as 'nice' as I'd expect it to be if it was a metagenomic sample: among others, GC-content, overrepresented sequences and
per base sequence content get warnings in all samples. Also, processing has almost no effect on the quality.
I am aware that the fastqc output of RNA-Seq data differs from metagenomic data. For example, I'd expect bias in the overrepresented sequences due to different expression levels of
genes etc. However, I'd like to get that confirmed by someone more experienced than me to know that I'm not on the wrong track here.
This is the fastqc plots for one sample before processing.
After removal of rRNA and adapter sequences as well as some trimming and removal of low quality reads the fastqc stats look like this.
I'd appreciate any (useful) comments.
Best regards,
Tim
I am trying to do some DE-analysis with different TruSeq paired-end samples. As I'm new to RNA-Seq I'd like to ask for some advice/opinions on my data and my quality control settings.
I use fastqc for quality control and none of my samples look as 'nice' as I'd expect it to be if it was a metagenomic sample: among others, GC-content, overrepresented sequences and
per base sequence content get warnings in all samples. Also, processing has almost no effect on the quality.
I am aware that the fastqc output of RNA-Seq data differs from metagenomic data. For example, I'd expect bias in the overrepresented sequences due to different expression levels of
genes etc. However, I'd like to get that confirmed by someone more experienced than me to know that I'm not on the wrong track here.
This is the fastqc plots for one sample before processing.
After removal of rRNA and adapter sequences as well as some trimming and removal of low quality reads the fastqc stats look like this.
I'd appreciate any (useful) comments.
Best regards,
Tim