Question: What can I use to identify primer sequences in my fasta files?
gravatar for c.older
17 months ago by
c.older0 wrote:

I have NGS data of the V4 region of 16s rRNA but I am not aware of the primers used. I'm pretty sure the primer sequences are still in the files because the data is unprocessed, and I was able to remove the primers [of known sequences] for another data set from the same sequencer So wondering if there are tools that can help me figure out what these sequences are so that I can remove them appropriately? I was considering just trimming 20 bp from each end, but would prefer to remove the specific sequences. I have tried to align multiple sequences and see if I can find a common sequence, and I think I have found the reverse but am not confident in the forward..

sequencing sequence next-gen • 1.2k views
ADD COMMENTlink modified 17 months ago by Friederike5.3k • written 17 months ago by c.older0

I am not an expert but trim_galore documentation says that it predicts and removes adapters automatically and then does the fastqc. You need to have cutadapt and fastqc libraries to be able to run it.

ADD REPLYlink written 17 months ago by piyushjo220

If you have paired-end reads and if enough reads have inserts shorter than read length then you can do this with BBTools: in1=r1.fq in2=r2.fq outa=adapters.fa

outa file contain adapter sequences.

ADD REPLYlink written 17 months ago by genomax78k
gravatar for Friederike
17 months ago by
United States
Friederike5.3k wrote:

Have you tried cutadapt? Sounds like it should be up the job.

ADD COMMENTlink written 17 months ago by Friederike5.3k
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