Question: (Closed) Converting .sra to fatsq
0
gravatar for mp
14 months ago by
mp0
mp0 wrote:

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

fastqc fastq sra geo • 492 views
ADD COMMENTlink modified 14 months ago by b.nota3.7k • written 14 months ago by mp0
1

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!

ADD REPLYlink modified 14 months ago • written 14 months ago by genomax46k

Which command are you using to convert the reads?

However, I suggest you to give a look at this post, where it is explained how to proceed with SRA

Best,

How to download raw sequence data from GEO/SRA

ADD REPLYlink written 14 months ago by IP350

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

ADD REPLYlink written 14 months ago by WouterDeCoster27k
0
gravatar for b.nota
14 months ago by
b.nota3.7k
Netherlands
b.nota3.7k wrote:

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

ADD COMMENTlink modified 14 months ago • written 14 months ago by b.nota3.7k
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