Hello everyone,
I just received a set of sequences from an RNA-Seq experiment.
Illumina HiSeq 2000, pair-end sequencing was performed.
Quality of R1 sequences look good, but R2 not so... (please, see attached reports as an example). R2 shows a lot of biased.
My question is how to proceed with these data? Do I need to ask the Genomic platform to resequence, or I can just treat the R2 sequences in order to get rid of the bad quality nucleotides? I am thinking that I could just trim 5 nts at the 5' end and 25 at the 3'end and then continuing with mapping and DEG analysis.
What do you think?
Thanks in advance
I just received a set of sequences from an RNA-Seq experiment.
Illumina HiSeq 2000, pair-end sequencing was performed.
Quality of R1 sequences look good, but R2 not so... (please, see attached reports as an example). R2 shows a lot of biased.
My question is how to proceed with these data? Do I need to ask the Genomic platform to resequence, or I can just treat the R2 sequences in order to get rid of the bad quality nucleotides? I am thinking that I could just trim 5 nts at the 5' end and 25 at the 3'end and then continuing with mapping and DEG analysis.
What do you think?
Thanks in advance
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