Question: fastqc output analysis
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gravatar for askari.arezou94
14 days ago by
IRAN/AHVAZ
askari.arezou9430 wrote:

enter image description here

what is your idea about this output? I should trim this? my data is transcriptome and the length of reads are 50

sequencing rna-seq assembly • 96 views
ADD COMMENTlink modified 14 days ago by ATpoint44k • written 14 days ago by askari.arezou9430

there is a bit too little detail in your post to tell I'm afraid.

But do take into account that fastQC is very stringent (and it's base line is DNAseq), so that you will only have green checks is rather the exception than rule, especially when inputting RNAseq data. (eg. for RNAseq, due to its nature you will always have the red check for the duplication levels section)

ADD REPLYlink written 14 days ago by lieven.sterck9.5k

thank you so much for good comment.

ADD REPLYlink written 14 days ago by askari.arezou9430

Hi,

Without showing the plots it is difficult to comment. I would say that (depending also on the library prep) it is normal to have a warning/error (orange/read) flags on Per base sequence content, specially a bias in the beginning that depends on the library prep, as well as Sequence Duplication Levels due to some intrinsic high transcripts and/or PCR amplification.

I would say that the other warnings/error flags can be more worrisome, but of course it depends on the library and the data. For instance the flag Overrepresented sequences can be due to some adapters that you did not remove, etc.

Read more about these details and interpretations in this nice tutorial/course: hbctraining

I hope this helps,

António

ADD REPLYlink written 14 days ago by antonioggsousa1.9k

ok, I can find my responses in this comment. thank you

ADD REPLYlink written 14 days ago by askari.arezou9430
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