how to run star-fusion using star *.aligned.sortedByCoord.out.bam

[Tadashi Kondo]

Hi! 

I would like to run star-fusion using aligned.sortedByCoord.out.bam as output from STAR.

I thought that change from the bam file to fastq file was conducted with bedtools bamtofastq. Then, I run star-fusion with the exchanged files.

Time of exchange took long time.

Would you like to tell me if you have idea to run star-fusion using aligned.sortedBycoord.bam files ?

Sincerely yours,

Ray

[Brian Haas]

Hi,

It only uses fastqs as input (or if you've run STAR with settings on our wiki that will produce the chimeric output file, you can just feed it the chimeric output file).

If you need to remake fastqs from aligned bams, be sure that all the unaligned reads are still in the bam, and what I'd do is to to revert it to an unaligned bam before converting to fastq. PicardTools is good for this.

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Brian J. Haas
The Broad Institute
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[Rayandkay]

Dear Brian,

Thanks for your quick reply.

I'll try to use Picard to reconstruct fastq from bam files.

Then I ran like an attached cord:

./STAR-Fusion --genome_lib_dir ctat-genome-lib-builder/ctat_genome_lib_build_dir --left_fq /home/renoguch/miniconda3/envs/picard/bin/R1.fq --right_fq /home/renoguch/miniconda3/envs/picard/bin/R2.fq --output_dir ./DFSP_NCC020/
* Running CMD: /home/renoguch/miniconda3/envs/star-fusion2/bin/STAR --genomeDir /rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion2/lib/STAR-Fusion/ctat-genome-lib-builder/ctat_genome_lib_build_dir/ref_genome.fa.star.idx  --outReadsUnmapped None  --chimSegmentMin 12  --chimJunctionOverhangMin 12  --chimOutJunctionFormat 1  --alignSJDBoverhangMin 10  --alignMatesGapMax 100000  --alignIntronMax 100000  --alignSJstitchMismatchNmax 5 -1 5 5  --runThreadN 4 --outSAMstrandField intronMotif  --outSAMunmapped Within  --outSAMtype BAM Unsorted  --readFilesIn /home/renoguch/miniconda3/envs/picard/bin/R1.fq /home/renoguch/miniconda3/envs/picard/bin/R2.fq  --outSAMattrRGline ID:GRPundef  --chimMultimapScoreRange 10 --chimMultimapNmax 10 --chimNonchimScoreDropMin 10  --peOverlapNbasesMin 12 --peOverlapMMp 0.1  --genomeLoad NoSharedMemory  --twopassMode Basic
Jul 04 06:24:50 ..... started STAR run
Jul 04 06:24:50 ..... loading genome
Jul 04 06:24:52 ..... started 1st pass mapping

stopped at "started 1st pass mapping"

Under 50G RAM, I ran at this time.

What should I do to solve stopping ?

Many thanks,

Ray

2023年6月23日金曜日 21:59:27 UTC+9 bh...@broadinstitute.org:

[Brian Haas]

Did you hit a time limit on a HPC grid submission? Were there any
errors encountered? If it crashes, there's usually a bunch of related
messages.

best,

~b

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