Extract Genomic DNA error with custom genome

Question: Extract Genomic DNA error with custom genome

3.8 years ago by

European Union

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

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modified 3.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.8 years ago by skeffington • 0

3.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link modified 18 months ago • written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

That worked! Many thanks! Alastair

ADD REPLY • link written 3.7 years ago by skeffington • 0

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

ADD REPLY • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

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:

Wrap the sequence content at 80 bases
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 REPLY • link modified 18 months ago • written 22 months ago by Jennifer Hillman Jackson ♦ 25k

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