Analyzing FastQC report

Question

[rsafavi]

Hi everyone,

I am new to RNAseq analysis, and would very much appriciate if I can get some help with the preprocessing step.

I used fastqc to look at my mouse RNAseq data, and I am getting many errors.

The basic statistics is fine: Total Sequences 57457361 Sequences flagged as poor quality 0 Sequence length 150 %GC 49

[PASS]Basic Statistics

[PASS]Per base sequence quality

[PASS]Per tile sequence quality

[PASS]Per sequence quality scores

[FAIL]Per base sequence content

[FAIL]Per sequence GC content

[PASS]Per base N content

[PASS]Sequence Length Distribution

[FAIL]Sequence Duplication Levels

[FAIL]Overrepresented sequences

[PASS]Adapter Content

Following images represents the failed steps:

Should I be worried of these errors? or should I proceed with the alignment?

Thanks!

Answer 1

[GenoMax]

Look through posts on this site for insight into various FastQC observations. You do appear to have poly-T/A stretches so these libraries are not great quality.

You should proceed with scanning/trimming of the data before you do alignments. I recommend bbduk.sh from BBMap suite.