How to convert fasterq File into fastq files ?
So I have two fasterq files such as :-
20900104398_S66_L001_R1_001.fasterq
20900104398_S66_L001_R2_001.fasterq
I want to convert them into fastq files so that I can start doing downstream analysis in my pipeline. I tried using fasterq-dump (as it was the only thing I found until now). But using that is giving me an error
2022-11-15T07:14:08 fasterq-dump.3.0.0 err: name not found while resolving query within virtual file system module - failed to resolve accession '/mnt/hdd/Data/20900104398_S66_L001_R1_001' - Cannot resolve accession ( 404 )
2022-11-15T07:14:08 fasterq-dump.3.0.0 err: extract_acc2( '/mnt/hdd/Data/20900104398_S66_L001_R1_001' ).VFSManagerExtractAccessionOrOID() -> RC(rcVFS,rcPath,rcConstructing,rcParam,rcIncorrect)
fasterq-dump quit with error code 3
Is there any other tool to convert them?
Thank you!
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fasterq-dump quit with error code 3
written by Aki •
the error looks like more a filesystem problem than a software error
Okay. This is the first time I have encountered this type of filetype. So the error is also confusing.
Just to clarify, are you downloading data from NCBI, because it seems to me that this is data (based on file name) right from a local sequencer?
No, I didn't download the data from NCBI. The client gave it to me.
Then you don't have to run this tool. fasterq-dump is a tool to fetch published NGS data from NCBI. What did you expect would it do?
Does
head 20900104398_S66_L001_R1_001.fasterqshow binary characters like example here Tools for fasterq file? ?What does the command
file 20900104398_S66_L001_R1_001.fasterqshow?Yes the command
head 20900104398_S66_L001_R1_001.fasterqis showing just like the link to attached.And
file 20900104398_S66_L001_R1_001.fasterqis showing20900104398_S66_L001_R1_001.fasterq: Progressive Graphics image data,We have two examples of files (one from other thread) in a previously unseen format. What kind of sequencer is this data from (file name seems to be in Illumina format)? I wonder if it is from a new batch of sequencers that were recently announced. If so it may need re-processing to generate sequence data.