Entering edit mode
2.6 years ago
nicole.kavanagh
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0
Hi there,
Sorry if this is a stupid question, but I'm hoping someone can help me. I'm trying to access fastq files from the SRA run browser (see this link: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3138122). However, all 53 samples seem to be contained in one file when I download it which is a .1 extension. Has anyone had any experience with opening this to access the fastq files or converting it in to the correct format? I also tried to download it using Amazon Web Services (AWS), but again this just gives me a .man extension which I am not sure what to do with. Any help with this issue would be greatly appreciated, I am new to all of this and apologies if it is an easy fix.
Thanks.
Thank you so much for your reply and your advice! I have to agree, the SRA website is very hard to navigate. I just tried to get the files using the FTP links on command line, but it keeps failing to connect and timing out unfortunately. I'm not sure if this is a firewall issue in our institution or maybe there is an issue with the FTP-link itself.
It works on my machine, could indeed by an issue at your side.
Thank you so much for your reply, it was just a firewall issue but it has been resolved. I've downloaded all the files now using ftp and the links you gave me so thanks!
They appear to have downloaded as two large fast q files (forward and reverse) - do you normally use command line to split them up into their respective sample files?
Yes, this is how it normally is. Usually the fastq files represent everything that has been sequenced with the same Illumina barcode on that particular run, unless the authors have merged multiple runs into the same fastq file and uploaded that, which is at least not super standard. Why do you think that there are multiple samples in that file?