help with extract reads from srr accession

I used Faster Download and Extract Reads in FASTQ format from NCBI SRA (Galaxy Version 2.10.4+galaxy1) and obtained 4 outputs (image attached) what is the meaning of each output and my data is paired end so which file i should use for downstream analysis? and the 4 dumped file is uploaded from single srr accession. Thank you.

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The data retrieval appears to be still in progress in your screenshot.

Allow the process to complete. This tool will place your data into Dataset Collections with this tool. The tool form explains and once you review the results, that help will more easily understood.

If you do not want to use Dataset Collections, but an individual dataset or a paired set of datasets (may be appropriate if you have a single accession), then use this tool instead Download and Extract Reads in FASTA/Q format from NCBI SRA.

Be aware that you may need to reformat the output from the alternative tool in order to prepare fastq data to be appropriate for use with tools. FAQ: Reformatting fastq data loaded with NCBI SRA. Specifically, the data may be interlaced – you’ll need to check your data and check the requirements for the tool you plan to use next, then making adjustments as needed.

I’ve added a tag to your post “dataset-collection”. Please review prior Q&A for help with using data bundled into collections, including tutorials.


Thank you for reply is it necessary to separate the single accession file to split it in two or i can use trimmomatic without splitting ? in trimmomatic there are three option single end, paired end as two seprate and paired end as collection . i have single accession file and want to proceed with trimming option is it neccessary to go for de-interlacer option or i can proceed directly with the paired end option but I don’t know which paired end option to choose (two separate or paired end as collection). and what does the below input means
Input FASTQ file (R1/first of pair):
Input FASTQ file (R2/second of pair): means?

Thank you

Consolidating this follow-up question back into original topic. See: