Star-Fusion: A last-matching gene pairs file - in Galaxy you can create such files with the ncbi_blast

Question: Star-Fusion: A last-matching gene pairs file - in Galaxy you can create such files with the ncbi_blast_plus tool suite containing blastn: ....

5 months ago by

andrewzlobin • 20

andrewzlobin • 20 wrote:

I am running Star-fusion on rat genome

Position:

A last-matching gene pairs file - in Galaxy you can create such files with the ncbi_blast_plus tool suite containing blastn: https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus

not clear to me.

I tried to generate the file like advised, it crashed. What do I do?

Thanks AZ

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modified 4 months ago • written 5 months ago by andrewzlobin • 20

5 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

It looks like the BLASTN job failed, so that cannot be used as input Star-Fusion. My guess is that the failure is due to the fasta identifier lines containing description content (is not formatted correctly for a custom genome).

Also, the fasta reference supplied does not appear to be based on the same rat genome/build as the reference annotation dataset, so even if you had BLASTN succeed, a genome mismatch problem would later come up with Star-Fusion.

The genes.gft annotation you is from iGenomes and from one of the UCSC builds they host (rn4, rn5, or rn6) -- correct? These genome build/versions are all natively indexed for Star-Fusion already at Galaxy Main https://usegalaxy.org, so there is no need to do the BLASTN step.

Solution: Use the option Source for sequence to search > Locally cashed sequences and set the rnX version to be the same genome build/version as the source for the genes.gtf.

Support FAQs: https://galaxyproject.org/support/

Thanks! Jen, Galaxy team

ADD COMMENT • link written 5 months ago by Jennifer Hillman Jackson ♦ 25k

5 months ago by

andrewzlobin • 20

andrewzlobin • 20 wrote:

Thanks a lot, But it looks to me that locally cashed sequences for Rat includes only rn5. Is this correct?

Thanks Andre

ADD COMMENT • link written 5 months ago by andrewzlobin • 20

rn6 is available for this tool - type into the box to do a "search" and find it. The description has a slightly different format than the earlier builds and might be missed with a scroll.

ADD REPLY • link written 5 months ago by Jennifer Hillman Jackson ♦ 25k

5 months ago by

andrewzlobin • 20

andrewzlobin • 20 wrote:

Thanks a lot. It did not work so far. I am afraid this is RNA STAR program problem. When I ran RNA STAR I took Use a build in index I could not "Use genome reference with builtin gene model", as "Select reference genome" is empty, So I use Genome reference WITHOUT builtin gene model: Select reference genome Rat Jun.2014 (RGSC 6.0/rn6) (rn6). Gene model (gff3,gtf) file for splice junctions Rattus_norvegicus_UCSC_rn6.tar Could it be a problem? If it is,then how to I use "builtin reference

Also when I ran RNA STAR I get: This job was terminated because it used more memory than it was allocated. Please click the bug icon to report this problem if you need help.

ADD COMMENT • link written 5 months ago by andrewzlobin • 20

4 months ago by

andrewzlobin • 20

andrewzlobin • 20 wrote:

Dear Jennifer, My question is: When I ran RNA STAR I could not "Use genome reference with builtin gene model", as "Select reference genome" is empty and, so I use Genome reference WITHOUT builtin gene model: Select reference genome Rat Jun.2014 (RGSC 6.0/rn6) (rn6). Gene model (gff3,gtf) file for splice junctions Rattus_norvegicus_UCSC_rn6.tar and so on. Could it be a problem? Should I use "Use genome reference with builtin gene model"? If YES, than how? Thanks Andrew

ADD COMMENT • link written 4 months ago by andrewzlobin • 20

4 months ago by

andrewzlobin • 20

andrewzlobin • 20 wrote:

I am lost I can not find out how I created genes.gft, neither AABR07.fasta for rat. Could you explain please?

Thanks Andre

ADD COMMENT • link written 4 months ago by andrewzlobin • 20

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