Dear Jennifer,
My .fasta reference genome is like this:
'gi|289546492|ref|NC_011420.2| Rhodospirillum centenum SW chromosome,
complete genome'
and in the SAM file generated by BOWTIE it says:
@SQ SN:gi|289546492|ref|NC_011420.2|LN:4355543
So I think they are all the same as
Hello,
The first thing to double check is that the chromosome identifier is an
exact match between the reference genome and the reference annotation.
The GFF3 file is naming the chromosome NC_011420.2.
The reference annotation chromosome should be named exactly the same
way. Check this in
Hi,
I'm getting this cuffmerge error on our local Galaxy instance. I
assume it is because it doesn't have the hg19 reference genome. Can
you please tell me how I would include into this Galaxy
installation?
Thank you.
Hello,
Instructions for including a new genome indexed for tools, including how
to download the same indexes used on the public Main Galaxy instance
hosted at http://usegalaxy.org, are in these wikis:
http://wiki.g2.bx.psu.edu/Admin/Data%20Integration
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