Extracting sequencing data from SRA accesion

Question

[ashwing.kofficial]

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

Answer 1

[GenoMax]

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.

[ashwing.kofficial]

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.

Answer 2

[noahhelton98]

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.

[ashwing.kofficial]

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.