What bam file readers that can read remote ftp/http files? I only know of samtools, but I would like to know of other tools that can also read remote files through ftp/http or other protocols. By remote access, I mean something like this:
samtools view ftp://ftp.site.com/file.bam chrN:1234-3456
samtools view http://www.site.com/file.bam chrN:1234-3456
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I am not aware of those tools. However you can easily combine wget, curl, lftp or any download tools with samtools in a shell, perl, or python script to get the job done.
that is not the same thing because you don't need to download the entire file to do a remote viewing - whereas your solution does that - the downloads could be impractically large
You are right, about the possibility of viewing files without download the whole things. But from my experience, it is better to load everything to my workstation and do whatever I like afterward.
I believe IGV will read remote files via http or ftp
Chris, how does IGV work for you when you view a very large SAM file, i.e whole exome? I have 24GB of RAM on a workstation and the software works at unacceptable speed.
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