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Barcode and Adapter sequences in sRNAseq data

Hi Everyone, I am new to RNAseq data. I am working on sRNAseq data and I am trying to start with adapter trimming part. I want to understand whether I have to remove the barcode region (the first 6 bases) from the reads in my sRNAseq data. I have done the alignment of 3 different reads and adapter, as seen here https://ibb.co/mknT7Q . I want to know the tools I can use to trim the barcode sequences( or may be I do not have to? please clarify!) and the adapter region. Can someone please explain. Thank you.

rna-seq
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written by MAPK MAPK

So you basically want to keep the part of the read that is to the left of the adapter position? If that is the case then you can use bbduk from BBMap with the literal=adapter_sequence option. Use the ktrim=r and ktrim=l combination to capture the part of the read you want.

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written by GenoMax GenoMax

@genomax Thank you for your answer. Yes I want to remove the adapter sequences and keep the actual reads only. As in this fastq file here-https://ibb.co/iENdP5, is it not that I also have to trim the 6 bases (ACTTGA bases) on the second line in fastq file?

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written by MAPK MAPK

Can you clarify if sRNA is single cell RNA data or something else?

Just to confirm you are expecting your read of interest to be on the left side of where ever you find the adapter in the read, correct? In that case those ACTTGA bases may be real data and you would want/need to keep it?

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written by GenoMax GenoMax

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