Extracting sequencing data from SRA accesion
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3.4 years ago

I am currently trying to extract reads from SRA accesion number in the galaxy program using the tool but the job has been running for a long time, is there any other alternative way I could extract, I do know R but not well versed with it . Also it would helpful if there is a way I could check the quality control of the dataset without having the sequencing data

rna-seq next-gen sequence • 695 views
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3.4 years ago
GenoMax 144k

If you ultimately need to use galaxy then it may be best to leave the program running the way it is.

You could download the sequence data directly from EBI-ENA and then upload that to Galaxy. Depending on the bandwidth you have available this may or may not yield time improvement. Are you using PSU public or a private galaxy server?

I could check the quality control of the dataset without having the sequencing data

Not in any meaningful way. NCBI pre-screens the data to see what genera are represented in the data but that is about all the pre-created QC you are going to see without the actual data in hand.

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Hello, Thanks for taking your time, I have registered an account in Galaxy, I don't know if that counts as private galaxy server and thanks for the info about QC.

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3.4 years ago
noahhelton98 ▴ 80

I usually use fastq-dump from the SRA tool-kit (https://www.ncbi.nlm.nih.gov/books/NBK158900/) to extract my reads - This usually works a little faster than galaxy, but requires some knowledge of the command line and the right environment set up on your computer. If your institution has an HPC, I would imagine this toolkit is already installed and you can just run a bash script to get all the reads you are looking for.

Also, look at the SRA run selector and click on a run to get a rough idea of the quality of the reads, but like @GenoMax stated this will not be too meaningful and you should do fastQC once you have the sequence data in order to actually assess the quality.

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Hello, thanks for taking your time, I already do use FastQC tool in galaxy for the quality check , I just wanted to know whether there was an alterative and thanks for your tip on extracting reads.

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