Question: rna seq read cleaning
gravatar for rahul.sg98
20 months ago by
rahul.sg980 wrote:

Please suggest me a tool for removing bacterial contamination from RNA seq reads before assembly.

rna-seq alignment • 692 views
ADD COMMENTlink modified 19 months ago by luca.marisaldi30 • written 20 months ago by rahul.sg980
gravatar for Mo Heydarian
20 months ago by
Mo Heydarian830
United States
Mo Heydarian830 wrote:

Hello, Can you provide some more information on what data you would like to remove bacterial reads from and what your desired outcome is? This will help in answering your question.

Look forward to hearing from you again!

Thanks for using Galaxy!

Cheers, Mo Heydarian

ADD COMMENTlink written 20 months ago by Mo Heydarian830

Hi, Thank you very much for your kind response. Actually, I have downloaded pair end RNA seq reads for assembly. reads were cleaned by trimmomatics: - adapter cleaning,q20, max read length 30bp. Assembled by Trinity with Group pairs distance- 500 bp,path reinforcement:- 50bp,min legth-200bp, assembled sequences were used for cap3 :- overlap 40bp, 90% identity. Then used for cegma and busco. But my completeness score for both cegma and busco is not coming more than 78% after repeated optimisation. Some people suggested me bacterial read cleaning, but don't know what tool to use and whether will it be available on the galaxy.

ADD REPLYlink written 20 months ago by rahul.sg980
gravatar for luca.marisaldi
19 months ago by
luca.marisaldi30 wrote:


Did you check the quality of the reads before and after Trimmomatic cleaning/filtering ?

FastQC is an excellent option and as far as I know you can have a first check towards this kind of (supposed?) contamination by checking the section "Overrepresented sequences". Eventually you can quickly blast these sequences in order to get some clues.

Maybe this can be of some help,


ADD COMMENTlink written 19 months ago by luca.marisaldi30
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