Question: Analyzing FastQC report
0
gravatar for rsafavi
12 months ago by
rsafavi40
rsafavi40 wrote:

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:

duplication_levels per_base_sequence_content per_sequence_gc_content Screen_Shot_2018_06_06_at_4_01_58_PM

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

Thanks!

fastqc rna-seq • 732 views
ADD COMMENTlink written 12 months ago by rsafavi40
1
gravatar for genomax
12 months ago by
genomax68k
United States
genomax68k wrote:

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.

ADD COMMENTlink written 12 months ago by genomax68k
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