Question: Extracting files from sequencing core
0
gravatar for rptiluswatson
6 weeks ago by
rptiluswatson0 wrote:

Good Evening, I just received my sequencing data with no directions from the sequencing core on how to download the files. And I do not have access to a bioinformatician to help me out. I am trying to do RNAseq analysis on galaxy but I am stuck at step 1.

The core sent me a bunch of files online with the names Mydata.fastq.gz.webloc I was trying to first move them to my external harddrive for safekeeping. Right now each file takes about 40 minutes to upload to my hard drive and I have 29 files left to upload. So far I have been getting them onto the hard drive by double clicking save as Mydata.fastq. I was wondering if there is a faster way to get them all onto my external hard drive?

I'm sure there has to be a smarter way to do this could you point me in the right direction? Also I am not sure exactly how I should get the .fastq files onto galaxy. I noticed the example data from the tutorials are called fastqsanger. Once I get the data do I then need to change all of the file extensions to fastqsanger in order to upload them into galaxy? If so, is there a smart way for me to do this as well?

I have barely any skills using the command line so if that is the only way to do this efficiently I will need a lot of guidance. Thank you so much for your help, Pam

rna-seq • 58 views
ADD COMMENTlink modified 6 weeks ago by Devon Ryan1.7k • written 6 weeks ago by rptiluswatson0
1
gravatar for Devon Ryan
6 weeks ago by
Devon Ryan1.7k
Germany
Devon Ryan1.7k wrote:

I was wondering if there is a faster way to get them all onto my external hard drive?

Give the sequencing facility your hard drive. They should be able to just copy everything on more quickly.

Once I get the data do I then need to change all of the file extensions to fastqsanger in order to upload them into galaxy?

File extensions don't actually mean anything on modern computers. Upload the files to Galaxy via FTP and then import them. You can manually set the datatype to "fastqsanger.gz", which is what you actually received (not sure why you stripped the .gz extension off from the links). You can use FileZilla or any other FTP client to transfer the files.

ADD COMMENTlink written 6 weeks ago by Devon Ryan1.7k
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