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..
•
written
by
c.older •
1 answer
Have you tried cutadapt? Sounds like it should be up the job.
Log in to answer this question.
-
Meta-analysis using 16S rRNA NGS data
written by bala •
-
16S rRNA merge forward and reverse primers
written by ddowlin
-
Preparing 16S gene amplicon (metagenomic) sequencing data for submission to ENA
written by KQUB •
-
Taking out 16S V3 region from V3-V4 sequence
written by aelitahuang •
-
error running bbduk to trim primers
written by caverill •
-
Length of the amplicon after trimming
written by life99945 •
-
Removing primers with degenerate codes
written by life99945 •
-
Finding adapters in sequences
written by genomics Newbie •
-
Primer sequences after PCR, Assembly and PCR
written by s.kyungyong64 •
-
How do i should proceed with 16S rRNA amplicon sequencing data from Illumina MiSeq using QIIME pipe…
written by antonioggsousa
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. https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md
If you have paired-end reads and if enough reads have inserts shorter than read length then you can do this with BBTools:
outafile contain adapter sequences.