On 12/23/13 7:12 PM, Yitian Xu wrote:
mm10 will be added as an indexed genome for Bowtie2/Tophat2 in the
I am a user from Cornell University. And you website is a
great help to me and my research. But there are two problems
with it I cannot figure out by myself, hoping you can help me.
1. When I uploading the data via FTP, there's option of
mouse reference genome mmp10. When I get to Tophat2, there's
only mmp9. Is there a problem that I use mmp10 at the
beginning and use mmp9 at tophat2? Or maybe you will update
It is very important to use the same version of a genome for all
steps in an analysis, otherwise the chromosomes and/or coordinates
will not match up. If doing RNA-seq analysis, the reference genome
used for mapping and the reference annotation (GTF/GFF3 file) should
all be the same. Ideally, you will want the input fastq sequences
also labeled as this same reference genome to stay organized, but
this is optional.
More RNA-seq help is here:
And the iGenomes reference GTF file for mm9 is already loaded as a
shared dataset, if you wish to use it, under "Shared Data -> Data
Libraries -> iGenomes".
It may be that you have deleted, but not permanently deleted,
histories or datasets. This wiki explains how to check:
2. I have around 50G space missing. I have one and only one
history (at least I can see) with 171.5G, but when I checked
my preference I used 225.2G. I don't know where the missing
50G count for then I don't know how to make room for my
ongoing analysis. My user name is douyadou. Can you help me
check for a min?
We will also examine your account for administrative issues and get
back to you if any anomalies are found.
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