How to trimm adapters from degradome

Question

[juan.crescente]

I want to trimm this degradome reads from its adapter:

https://trace.ncbi.nlm.nih.gov/Traces/sra/?view=search_seq_name&exp=SRX493831&run=&m=search&s=seq

Since the script (CleaveLand4) needs:

(adapter-trimmed degradome reads in FASTA format)

Thank you!

I've read somewhere that used 'vector strip’ in the EMBOSS package

[GenoMax]

If the linked data is standard Illumina run then you could use any standard trimming program (bbduk from BBMap suite, trimmomatic etc) to trim Illumina adapters and then convert the reads into fasta format (you can use reformat.sh from BBMap for that part).

I doubt vector strip from EMBOSS is going to be useful here.

[juan.crescente]

bbduk returns nothing. I'm running scripts/libs/bbmap/bbduk.sh in=data/degradome/sra_data.fasta -out clean.fq

[GenoMax]

You need to run bbduk on fastq format file and then convert it to fasta. Something like (adjust bbduk parameters as needed).

bbduk.sh in=your_original.fq out=stdout.fq ref=/path_to/bbmap/resources/adapters.fa ktrim=r k=15 | reformat.sh in=stdin.fq out=cleaned.fa

[juan.crescente]

where do I get the adapters.fa file?

[GenoMax]

It is included with BBMap in a directory called "resources". That is why I had the path_to which you should replace with a real path on your computer.