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Converting .sra to fatsq

Hi everyone. I downloaded some .sra files from GEO and I want to view them on FASTQC. In order to do that I think I need to convert my .sra files to bam, sam or fastq. I downloaded the SRA Toolkit (MacOS 64 bit architecture) to convert them to fastq. I keep running the commands found in the README-vdb-config file but i keep getting ''command not found'' on the Terminal. Any suggestions on how to convert .sra to fastq? Thanks

geo sra fastq fastqc
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updated by Benn Benn • written by mp • mp

Hello maria.perd17!

This question has been asked multiple times.
There are tutorials for this: https://www.ncbi.nlm.nih.gov/books/NBK158900/
Converting sra to fastq

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by GenoMax GenoMax

Your problem is more a software-installation problem, the executables you downloaded are not in $PATH and therefore not found by your operating system.

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written by WouterDeCoster WouterDeCoster

1 answer

Best thing to do is not to download the sra files from NCBI, but use fastq-dump of the SRA toolkit to get them for you. Then you don't need to convert them because they will be fq format directly.

See previous posts, e.g., A: Is It Fastq Format

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written by Benn Benn

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