Help on building genome_lib_dir for STAR-Fusion (hg38)

[Job van Riet]

Dear all,

Could someone shed some light or guide me to a manual on how to generate a genome_lib_dir for another reference genome used in STAR-Fusion, in this case Homo sapiens hg38.
I take it I'm first supposed to run the prep_genome_lib.pl script in the FusionFilter package but unfortunately I'm stuck on the --blast_pairs parameter. Am I meant to run blastn (-outfmt 6) on all transcripts present in the accompanying .gtf file (gencode_v23) and give this as input or am I misreading this parameter?

Thanks for any help!

Kind regards,

Job van Riet

[Brian Haas]

Hi Job,

I'll add documentation for this later today and post again once it's available.  It'll show up here:

https://github.com/FusionFilter/FusionFilter/wiki

stay tuned.

best,

~brian

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Brian J. Haas
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[Brian Haas]

Documentation is now available:

https://github.com/FusionFilter/FusionFilter/wiki

best,

~b

[Job van Riet]

Dear Brian,

Thanks for your quick reply and great help!
For others wanting to do the same thing using gencode annotation, remove the genes first:

grep -Pv '\tgene\t' gencode.v23.annotation.gtf > gencode.v23.annotation_transcriptsOnly.gtf

Kind regards,

Job van Riet

Op dinsdag 13 oktober 2015 03:43:44 UTC+2 schreef Brian Haas:

[Brian Haas]

You might also restrict it to the protein-coding transcripts.  Otherwise, there are more false positives to deal with.  I'll add a note about this in the documentation.

best,

~b

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[Foivos Gypas]

Hi Brian

I have a question related to the restriction to protein-coding transcripts.
In my case i want to look on snoRNA fusions. If I keep only protein coding transcripts, this means that I will not be able to identify fusions where snornas are involved? Right?

Thank you in advance for your response.

Best
Foivos

[Brian Haas]

Hi Foivos,

Yes, that's right.   I honestly have no idea how well it'll work w/ snoRNAs...   we focused entirely on coding genes and lncRNAs here.  

best,

~brian

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