Question: RNAseq fastqc report some failures, how to solve it?
0
gravatar for lovelymaoqin
4 weeks ago by
lovelymaoqin0 wrote:

I used fastqc to deal with my small RNA seq data, and according to the report I have some failures, do not know how to solve these situation. I post all the failure picture here, how someone can help me out? Thanks in advance.

adaptor content sequence duplicated! GC content per tile quality per base quality

rna-seq • 132 views
ADD COMMENTlink modified 4 weeks ago by h.mon31k • written 4 weeks ago by lovelymaoqin0

There are no actual failures with FastQC. The red X's mean that your data falls outside the bounds of intervals (which can be changed) which are mainly for genomic DNA sequencing. Small RNA seq data is expected to have ~25 bp of actual sequence and may contain adapter sequence (which will need to be trimmed out).

Use these directions to post images: How to add images to a Biostars post Once we see the images we can assist further.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by genomax91k

You can see that you need to trim your reads to remove Illumina small RNA adapter. This can be done by many tools. bbduk.sh from BBMap suite, cutadapt, trimmomatic and fastp.

ADD REPLYlink written 4 weeks ago by genomax91k
1
gravatar for swbarnes2
4 weeks ago by
swbarnes28.9k
United States
swbarnes28.9k wrote:

Adapter content might be a problem you can fix, but you should start by googling how to trim adapters, not wait around here for someone to spoon-feed you how to trim adapters.

ADD COMMENTlink written 4 weeks ago by swbarnes28.9k

fastp is probably the easiest way out.

ADD REPLYlink written 4 weeks ago by Dunois150
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