(cc'ing galaxy-user)
Sorry Jeremy, I'm being a bit dense here - where exactly are these tools in
the tool list - I can't find them...
David,
Both tools are located within the 'Operate on Genomic Intervals' menu. Also,
remember that tool search (Options - Show Tool Search) is useful for
Hi,
Yes, column 1 refers to the chromosome name and it must be the same throughout
(i.e. your hg19 reference file must call the chromosomes 1,2, 3 etc). A simpler
solution is to use a copy of hg19 that lists the chromosomes as 1, 2, 3 etc
instead of Chr1, Chr2 etc. Unfortunately I'm only in
Hi,
You need to supply a gene annotation file with cufflink to easily get the
gene-id information. Without it, cufflinks simply tries its best to figure out
what genes are present. The ensemble gtf file is quite a comprehensive one -
there is a link to it on the cufflinks manual page.
Good
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