Entering edit mode
4 months ago
Jjbox ▴ 40
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.
There is no
fasterqfile 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?
This is the head of this file. I thought I need to trim using something like bbuk?
Did you use
prefetchfrom SRAtoolkit to get these files? If so you may need to use
fasterq-dumpto extract the sequence files: https://github.com/ncbi/sra-tools/wiki/08.-prefetch-and-fasterq-dump
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
I guess the tool only accepts the file that starts with SRA.