Hello there,
I'm trying to download all the bam & bam.bai files of ENCODE's CSHL long RNA seq data using Perl from the UCSC FTP server here
I tried downloading one cell line at a time initially, but its too painstaking.. If anyone could please suggest a way or if anybody already has got a Perl script for this, could you please share? I'd be umpty grateful!
Best, Vaish
2 answers
Firefox download all is a great tip if you want to download them to your desktop. But if you want to download them in a server you need something else. There are many ways to do this and most of them are not very straight forward. I always use this simple trick to handle UCSC data downloads.
1. go to the folder
2. copy all the file names not the files
3. paste them in a text file and do this ..
4. ls -l | grep bam | awk '{print "wget "$9" ;"}' >> download.sh
5. now run sh download.sh
6. replace ";" with "&" if you want to do simultaneous downloads.
Simple isn't it ;)
You might want to download these BAM files to a different computer than you are sitting at. For instance, you might be on a laptop, but you have some "big iron" machine you wan to use to process the data sitting somewhere else that you might be ssh'd into.
If you're not married to the idea of scripting this yourself, and easy way to do this is to use Firefox with the DownThemAll plugin.
- Navigate to the ENCDOE CSHL Long RNA Seq page
- Go to
Tools > DownThemAll Tools> DownThemAlland enter*.bam,*.baiin theFast Filteringtext box at the bottom of the window that pops up. - Pick the appropriate folder you wan to save these fils in locally using the
Save files intext box - Click the
Start!button - ...
- Publish!
Please submit this as a new question to biostar and add some more detail to give us a better idea of what you are asking. For instane: I have no idea what you want to do when you say "run all the bam files together on samtools" -- doesn't make sense to me
Here's the one- Samtools And Cuffdiff
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