Mouse Fusion detection

[ninn...@gmail.com]

Dear all,

I would like to use the nice startfusiopn tool on mouse data.
For human I have used this as a resource lib:
https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/
but as it does not seem to be there for mouse, I was wondering if you made it, but did not provide it, or if I should do it myself?
If I should do it myself, how?:)

Thanks a lot for your help!

[Brian Haas]

Hi,

You can build a resource library for mouse by following the protocol here:

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

See the section under 'building a custom Fusionfilter Dataset'

best,

~brian

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Brian J. Haas
The Broad Institute
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[hideldi...@gmail.com]

Hello,

I would also like to use STAR-Fusion on mouse data, however I am having several difficulties in getting RepeatMasker to run in order to create my own mouse database.
Is there any way for anybody to upload the repeat-masked cDNA file for mm10 ?

Kind Regards,

Christoph

[ninn...@gmail.com]

Hi Christoph,

You can find this on the UCSC webpage:

Availability of repeat-masked data

	Question: "Are the repeat annotation files available for every chromosome?" Response: Yes, you can obtain the repeat-masked files via the Table Browser or from the organism's annotation database downloads directory. The RepeatMasker annotation tables are named chrN_rmsk (where N represents the chromosome number) and the Tandem Repeat Finder (TRF) tables are named simpleRepeat.

RepeatMasker version differences - UCSC vs. RepeatMasker website   Question: "When I run RepeatMasker independently from the RepeatMasker web server, my results vary from those of UCSC. What's the cause?" Response: UCSC occasionally uses updated versions of the RepeatMasker software and repeat libraries that are not yet available on the RepeatMasker website (see Repeat-masking data for more information).

Maybe this can help you further.

Best Nina

Am Dienstag, 7. Juni 2016 13:45:54 UTC+2 schrieb ninn...@gmail.com:

[Brian Haas]

I can try to build a mouse version.  Which mouse gencode release would be best for everyone?

Note, I don't have a test-bed for mouse, so this would all be for exploratory purposes.

~b

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[hideldi...@gmail.com]

Thank you both!

Brian, building a mouse version would be much appreciated.
I'd prefer the current Gencode release for mouse (M9).
Thank you again!

Regards

Christoph

Am Dienstag, 7. Juni 2016 13:45:54 UTC+2 schrieb ninn...@gmail.com:

[Brian Haas]

You got it.   I'll kick off the build shortly and see how it goes.

~b

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[Brian Haas]

Here's a build for mouse using M9/gencode

ftp://ftp.broadinstitute.org/pub/users/bhaas/tmp/MouseGencodeM9.tar.gz

All I did was build it, though, and haven't done any testing....  I don't have a set of mouse fusion transcripts to verify it works with as of yet.

Please let me know how it goes.

best,

~b

[Mahesh Vangala]

Hello Brian -

I am trying to build STAR_Fusion reference files with UCSC mm9 gtf and fasta files. In getting cDNA_seq.fasta using the command, I get following error

/zfs/cores/mbcf/mbcf-storage/devel/umv/software/miniconda3/lib/STAR-Fusion/FusionFilter/util/gtf_file_to_cDNA_seqs.pl /zfs/cores/mbcf/mbcf-storage/devel/umv/ref_files/mouse/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf /zfs/cores/mbcf/mbcf-storage/devel/umv/ref_files/mouse/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa 1> cDNA_seqs.fa

Error, no seek pos for acc: chr13_random at /zfs/cores/mbcf/mbcf-storage/devel/umv/software/miniconda3/lib/STAR-Fusion/FusionFilter/util/../lib/Fasta_retriever.pm line 71, <$fh> line 66909760.

        Fasta_retriever::get_seq(Fasta_retriever=HASH(0x26434c0), "chr13_random") called at /zfs/cores/mbcf/mbcf-storage/devel/umv/software/miniconda3/lib/STAR-Fusion/FusionFilter/util/gtf_file_to_cDNA_seqs.pl line 54

Let me know your thoughts.

Thanks,

Mahesh

[Mahesh Vangala]

Brian -

Ignore my question above.

It seems like I have in my gtf_file chr13_random info, however, I don't have the sequence chr13_random in my fasta file.

That did it.

Thanks,

Mahesh

[David Zhang]

Brian & Mahesh,

I met the same issue with:

Error, no seek pos for acc: chr1_GL456211_random at /opt/Anaconda2-4.3.0/lib/STAR-Fusion/FusionFilter/util/../lib/Fasta_retriever.pm line 71, <$fh> line 79772306.

        Fasta_retriever::get_seq(Fasta_retriever=HASH(0x1309e28), "chr1_GL456211_random") called at /opt/Anaconda2-4.3.0/lib/STAR-Fusion/FusionFilter/util/gtf_file_to_cDNA_seqs.pl line 54

How have you solved the problem?

Thanks,

David

[Brian Haas]

Hi

Just make sure the reference annotation (gtf) file that you're using is restricted to those features that map to contigs in your genome.fasta file.

best,

~brian

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