Problems of version between STAR and STAR-Fusion

[Tadashi Kondo]

Dear Brian,

I have another issue about problems of version between STAR and STAR-Fusion.

I have chimeric.out.juncsion file produced by outsourcing company (STAR version 2.5.2.a) and do not have raw data of the chimeric.out.junction file.

I would like to know sequence of breakpoint in fusion genes and learned with STAR-Fusion/util/append_fusion_brkpt_adjacent_sequence.pl   star-fusion.fusion_predictions.abridged.tsv $CTAT_GENOME_LIB from homepage.

I run as attached code: 

./STAR-Fusion --genome_lib_dir ctat-genome-lib-builder/ctat_genome_lib_build_dir -J /home/renoguch/input_noguchi/JSGC_DFSP_NCC020_01.Chimeric.out.junction --output_dir ./DFSP_NCC020

Error, file: /home/renoguch/input_noguchi/JSGC_DFSP_NCC020_01.Chimeric.out.junction doesn't have expected formatting.  Please be sure to use the STAR aligner with min version: 2.7.0f at ./STAR-Fusion line 1038.
        main::get_num_total_rnaseq_frags("/home/renoguch/input_noguchi/JSGC_DFSP_NCC020_01.Chimeric.out"...) called at ./STAR-Fusion line 523

To resolve this problem, I downgraded STAR and STAR-Fusion reflecting 2.5.2a.

But I cannot find download way to STAR 2.5.2a and STAR-Fusion_.

To solve this problem, what should I do ?

If I have a raw file of RNA-Seq, I'll run STAR and STAR-Fusion under newest version.

I just have Chimeric.out.junction, aligned.fortedBycoord.out.bam.

I just want to get an adjacent sequence of breakpoint finally.

Would you like to tell me your idea ?

Many thanks,

Ray 

[Brian Haas]

Hi Ray,

The best thing to do is to rerun the sample using the latest version,
assuming you can somehow get a hold of the original fastqs.

If it gives you trouble, you can make the fastqs available to me and
I'll run it through for you.

best,

~b

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--
--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

[Tadashi Kondo]

Dear Brain,

Thanks for your reply.

I got fastq files for running from the beginning.

I have one question.

I used environment for analysis under STAR-Fusion 1.6.0 and STAR 2.7.0f.

I tried to attain the files from https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.6/.

Using the link, file could not be found.

Would you like to a link connecting _genome_libs_StarFv1.6 ?

Many thanks,

Ray

2023年7月5日水曜日 0:13:15 UTC+9 bh...@broadinstitute.org:

[Brian Haas]

Hi Tadashi,

I had removed the old libs because they were taking up storage. I just
restored this set of libs. Hope it helps.

best,

~b

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