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rpetit3 / fastq-dl

Download FASTQ files from SRA or ENA repositories.
MIT License
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getting technical reads on fastq-dl #24

Closed reetm09 closed 6 months ago

reetm09 commented 11 months ago

Hi,

I'm trying to extract scRNA-seq fastq files and this tool works great! However, I was wondering if there was an option to get all the files in a paired-end sample? I only am getting one file back (SRR23891520.fastq.gz) but I believe I should get 2. There is a similar option on fasterq-dump by adding the "--include-technical" tag but I'd rather use fastq-dl and was curious if there was a way to do that through this package?

This is the command I ran: fastq-dl --provider SRA -a SRR23891520

Thanks so much for your help!

mranjan1 commented 11 months ago

Can you try the command below and see if it works?

fastq-dl --provider ENA -a PRJNA944177

mbhall88 commented 11 months ago

According to the SRA there is only one fastq https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR23891520&display=metadata

So this is either a problem from the submitter or the SRA? They seem to be very recently submitted, sometimes there can be a lag in SRA/ENA so maybe check again in a few days?

reetm09 commented 11 months ago

Hi @mranjan1 and @mbhall88,

Thanks so much! I tried the command but only got one file since I think there might be a lag in the upload of data, as you said. I was also wondering, if I did "--group-by-sample" how are the fastq's merged? Is it just concatenated at the end of the previous fastq, and is there a way to split it after the download?

Thanks!

rpetit3 commented 11 months ago

Hi @reetm09

--group-by-sample will take multiple Run accessions associated with a single Biosample accession and merge them into a single FASTQ. You are correct they are merged by concatenating the FASTQs together.

If there was a downstream need to split them afterwards, I would recommend against using --group-by-sample from the start.

There is usually a 1-2 week delay in syncing between ENA and SRA.

As to your original question about --include-technical, that would certainly be possible as an optional input. However, can you share some examples where you would use this? (I don't have any use cases in by day job).

Cheers, Robert

rpetit3 commented 6 months ago

Hi All!

I'm going to go ahead and close this, as I think things were resolved. Please feel free to reopen if not.

Cheers, Robert