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Question: clear overrepresented reads that arent adaptadors
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gravatar for biopili9
19 months ago by
biopili9 • 10
biopili9 • 10 wrote:

I am working in galaxy and I mapped the sequences with a genome of reference but the result show that only 27% of sequences were mapped. I did the trimmomatic but I cant clear the sequences overrepresent. wich tools I need to use for clear the specifics sequences

thanks
rna-seq • 547 views
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modified 19 months ago by luca.marisaldi • 30 • written 19 months ago by biopili9 • 10
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gravatar for luca.marisaldi
19 months ago by
luca.marisaldi • 30
luca.marisaldi • 30 wrote:

Hello!

Overrepresented sequences, among other things, might be an indicator of:

  • Contamination
  • Depending on the pre-processing cleaning might be a something related to an incomplete full elimination of ribosomal RNA
  • Presence of adapters (in this case FastQC should detect that)

I suggest to run a quality control before/after the cleaning steps, checking not only on the option "overrepresented sequences" but also other parameters such as "GC content" and "Kmer repetitions" (both provided by FastQC output). This way should give you some details about these sequences. As an option you can also blast them to quickly check what they are.

Once you understand that you can, in my opinion, proceed further.

Have a good day,

Luca
ADD COMMENT • link written 19 months ago by luca.marisaldi • 30
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