Question: Extract Genomic DNA error with custom genome
0
gravatar for skeffington
2.8 years ago by
European Union
skeffington0 wrote:

Hi,

I'm new to Galaxy, and I and trying to use the "extract genomic dna" tool. I would like to fetch the sequences defined in a cuffmerge output file (GTF format) from a custom genome file in my history (an indexed fasta file, genome.fa.fai). This is the same genome file that was used in the transcript assembly through TopHat, Cufflinks and Cuffmerge, The GTF seems ok - I can successfully view it in the Integrated Genome Browser. However, when I try to run "extract genomic DNA" I get the following error after a couple of minutes:

"Error running faToTwoBit. Expecting '>' line 1 of /galaxy-repl/main/files/010/529/dataset_10529575.dat"

Any help would be greatly appreciated!

Alastair

 

ADD COMMENTlink modified 2.8 years ago by Jennifer Hillman Jackson23k • written 2.8 years ago by skeffington0
2
gravatar for Jennifer Hillman Jackson
2.8 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Does your custom reference genome have description line in it? If you remove them, does the tool function correctly? How to remove description lines is explained here: Preparing and using a Custom Reference Genome or Build

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 6 months ago • written 2.8 years ago by Jennifer Hillman Jackson23k

That worked! Many thanks! Alastair

ADD REPLYlink written 2.8 years ago by skeffington0

Very glad! More details in case you run into other CG issues: https://biostar.usegalaxy.org/p/19322/#19350

ADD REPLYlink written 15 months ago by Jennifer Hillman Jackson23k

Update: The tool NormalizeFasta can now be used to reformat fasta files to be used for Custom Genomes/Builds in one step.

Options to use are:

  1. Wrap the sequence content at 80 bases
  2. Split the fasta title line at the first whitespace so that only a single word unique "identifier" remains

Preparing and using a Custom Reference Genome or Build

All Support

All Learn

ADD REPLYlink modified 6 months ago • written 10 months ago by Jennifer Hillman Jackson23k
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