Galaxy only showing single end data for paired end data with SRR download

Question

[hg1]

Dear galaxy users,

I have problem in downloading FASTQ data into galaxy. I only get data for single end and not the paired end from a dataset on ncbi.

Could anyone help explain why I am not getting a full fastq dump as the first screen for the rest of the SRR?

Here are some screen shots of how it looks when I load my data in. The first one look good but the rest of the SRR only has data for single end read and not full fastq data.

[Istvan Albert]

the most important information, the SRR number is not shown, make sure to mention that

[hg1]

Dear Istvan,

this is the SRR number: SRR8368419 Under single data it shows me this.

The problem is not only for that number is for most of them. I download the data by putting in the SRR number one at a time and loading them.

Furthermore, Its around 24 SRR ID I would like to have FASTq files for. Would there be a more efficient way to download it into galaxy without coming up with empty files.

this is the GSE number where all the SRR numbers I am using are under: GSE124174

[hg1]

I was thinking I would get this with the download (picture)

However, I don't get that with the rest of the SRR numbers.

I am new to galaxy and wondering if fastq files only show single end data for most SRR data which are paired end

[GenoMax]

This is a 10x scRNAseq dataset. I don't know if SRA download in galaxy can handle this properly.

[hg1]

how would you download it into Galaxy if not with SRA

Answer 1

[Istvan Albert]

you should look at the command that was run for you when the data is paired the --split-files flag is passed to the downloading tool.

the presence of that flag is what determines how the SRA file is unpacked

also it is probably best if you post on the Galaxy support forum, as the people there may have access to you history files

[hg1]

Thank you for the answer. I have written Galaxy support forum.

I am totally new to this programming and just now learning it. --split-files flag where do I see that?

[GenoMax]

--split-files flag where do I see that?

It is present under advanced options in Faster Download and Extract Reads in FASTQ tool in Galaxy. You will need to select the check box.

[hg1]

Dear GenoMax,

Thank you for the explanation. The command that was run was --split-3. However, that did not give me ant paired biological reads. I have now downloaded all the files as FASTqdump, now I would like to split it into R1 and R2. Is there a way to do that without re-downloading everything?

For the data I want to analyse I somehow only find 1 SRR accession number and that should give med R1 and R2 once downloaded into galaxy but unfortunately that's not happening.