Question: (Closed) adapter trimming PE RNA reads
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gravatar for rahmati.razieh83
2.0 years ago by
rahmati.razieh8330 wrote:

Dear all I have received some RNA reads prepared by SENSE mRNA-Seq Library Prep kit V2. After quality test of RNA seq reads with fastqc software, I found out that some reads showed red and some others yellow adapter content. What is common between the reads containing red and yellow adapter content is that, the fastqc adapter content graph is direct up to 13 th nucleotide and after 13th nucleotide there is a shift toward up but with more intensity for the reads with red adapter content. For the reads with red adapter content I removed them by removal of Illumina universal adapter via trimmomatic software using ILLUMINACLIP command. The fastQc quality test showed the removal of adapter and the adapter content got green. For the reads with yellow adapter content I can not find out if they contain adapter or not? I applied the removal of adapter command in trimmomatic for these reads (yellow adapter content). The results showed adapter removal for some reads but for some other reads the problem still persists and fastqc test still is showing yellow adapter content. So I completely got confused that what is this problem and why these graphs are still showing shift toward up. I need your help to find out the problem. my other question is about trimming instruction in the SENSE mRNA-Seq Library Prep kit V2 protocol. I tried to trim the reads again, this time by following the instruction in the protocol mentioning the removal of 9 nucleotide from R1 and 6 nucleotides from R2 reads. So I removed 9 nucleotides from 5' side of R1 and 6 nucleotides from 3' side of of R2. But it did not make sens and the problem of adapter content graph persists. Would you please guide me how can I solve this problem? and How can trim these reads?

rna-seq • 830 views
ADD COMMENTlink written 2.0 years ago by rahmati.razieh8330

Hello rahmati.razieh83!

Please do not post a question in multiple threads. We are closing this one since you have this thread open: trimming PE RNA Reads . You have not responded to the answers offered in that thread.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by genomax73k
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