Question: How to add reference annotation for Cufflinks to local Galaxy?
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gravatar for chaoyuan
2.5 years ago by
chaoyuan80
chaoyuan80 wrote:

I'm interested in using Cufflinks with reference annotation on my local Galaxy instance. I'm wondering how I can install reference annotation to my local Galaxy so that it's available to all the user? I tried searching for data_manager in the tool shed but I don't see such tool for fetching reference annotation.

I also tried downloading a reference annotation from the link provided on the Cufflinks website. I downloaded the UCSC version using the Get Data interface provided by Galaxy. I had this error:

Fatal error: Exit code 1 ()
Error running cufflinks.
return code = 1
Command line:
cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8 -G /home/joe/galaxy/database/files/000/dataset_25.dat /home/joe/galaxy/database/files/000/dataset_13.dat 
[16:34:05] Loading reference annotation.
Error parsing strand (3) from GFF line:
uc007aeu.1   chr1  -  3204562   3661579 3206102 3661429 3   3204562,3411782,3660632,    3207049,3411982,3661579,    Q5GH67  uc007aeu.1
cufflinks galaxy • 804 views
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by chaoyuan80
1
gravatar for chaoyuan
2.5 years ago by
chaoyuan80
chaoyuan80 wrote:

It appears that Cufflinks takes GFF3 files but not GTF files. I ended up downloading GFF3 files from enter link description here through Admin -> Data -> Data libraries. If access restriction is not set, it's available to all the users. From Shared Data -> Data Libraries, the reference annotation can be imported to history and used by Cufflinks. Cufflinks runs correctly with the GFF3 on my local galaxy server.

ADD COMMENTlink written 2.5 years ago by chaoyuan80
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