Tools for fasterq file?

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2.1 years ago

shinyjj ▴ 50

Hi all!

I want to trim these fasterq files. Some of them are long read rna-seq and some of them are short read rna-seq. Are there any tools to change these files into fastq file? I heard when trimming I should refer to .fasterq files as 'fastq.gz' even if they show as fasterq but having trouble what tools shall I use.

Thanks!

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trimming • 1.1k views

ADD COMMENT • link updated 2.0 years ago by NikhilP ▴ 20 • written 2.1 years ago by shinyjj ▴ 50

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There is no fasterq file format that I am aware of. Are these normal fastq format (https://en.wikipedia.org/wiki/FASTQ_format ) that contain short or long reads? What does a record look like? Show us head -n 4 26_R2_001.fasterq?

ADD REPLY • link 2.1 years ago by GenoMax 147k

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This is the head of this file. I thought I need to trim using something like bbuk? enter image description here

ADD REPLY • link 2.1 years ago by shinyjj ▴ 50

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Did you use prefetch from SRAtoolkit to get these files? If so you may need to use fasterq-dump to extract the sequence files: https://github.com/ncbi/sra-tools/wiki/08.-prefetch-and-fasterq-dump

ADD REPLY • link 2.1 years ago by GenoMax 147k

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I also have the same kind of file but with different name (it does not start with SRA) and I ran in the below error

2022-11-14T09:19:15 fasterq-dump.3.0.0 err: name not found while resolving query within virtual file system module - failed to resolve accession '20900104398' - Cannot resolve accession ( 404 )

I guess the tool only accepts the file that starts with SRA.

ADD REPLY • link 2.0 years ago by NikhilP ▴ 20

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