Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Fetch alignments using stitch Gene Blocks but all the gene-sequences are in '--------'
0
gravatar for yanghaobentley
3.0 years ago by
yanghaobentley • 0
China
yanghaobentley • 0 wrote:

I was using the GALAXY project (https://usegalaxy.org/) online server, the section is Fetch alignments -- > stitch Gene Blocks, and I wanted to extract some CDS genes in drosophila maf genome alignment file (from UCSC dm6 multiz27 way maf) according to a custom made BED file converted from GFF (the original file is from flybase dmel-all-r6.07.gff) file, however, as I do the extraction, the gene sequences I get are all in '-------'. As there is no genome build for dm6 in drosophila melanogaster, I build it myself via UCSC genome browser using the dm6 fasta genome sequences. Can anyone help me to sort out this problem? Thanks!
galaxy • 959 views
ADD COMMENT • link •
modified 3.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.0 years ago by yanghaobentley • 0
0
gravatar for Jennifer Hillman Jackson
3.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

It is unclear how a custom reference genome (fasta format) would be used with this tool.

It might be best to send in a shared history link and we can examine the inputs and processing. Paste the link, the problematic dataset numbers, and a link to this post in an email to galaxy-bugs@lists.galaxyproject.org

Thanks, Jen, Galaxy Team
ADD COMMENT • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k

Thank you for sending in the details. The problem with executed failed job was due to a format issue with the MAF input (possibly an incomplete file load, but this could not be determined due to the dataset being permanently deleted). The problem with unexecuted jobs using a different MAF input is a mismatch between the chromosome identifiers in the MAF versus the BED input (these were deleted before the jobs completed, but would have failed or produced unexpected results).

General tool troubleshooting help: Support#Error_from_tools

Please correct the format errors and try the tool again. If there is an error, submit the problem as a bug report directly from the history leaving all inputs and the error dataset undeleted. (To confirm: fasta input is not needed when using this tool).

ADD REPLY • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 172 users visited in the last hour