brianjohnhaas
commented
3 years ago Hi,
It would be best to use the STAR-Fusion pipeline to generate the bam, and then use that bam with the ctat mutations pipeline. Just be sure to include the STAR-Fusion parameter: --STAR_SortedByCoordinate (which it doesn't do by default, but will be needed for variant calling).
best,
~brian
On Mon, Sep 27, 2021 at 12:32 PM Tomas Bencomo @.***> wrote:
Hi,
I'm trying to profile fusions, mutations, and expression from RNA-Seq data using programs from the CTAT pipeline. For consistency I thought it would be optimal to have a single BAM for each sample that can be run through each program (STAR-Fusion, CTAT Mutation pipeline, RSEM or Salmon).
I see that ctat-mutations and STAR-Fusion by default both use FASTQs as input and output BAM files, although both pipelines can use BAM files as input. Does it make sense to run one pipeline first and then use the output BAM file for the other programs? For example, I could run STAR-Fusion using the FASTQ files and then use the resulting BAM as input to the mutation calling pipeline and RSEM. Is there an alternative ordering that would be better? My concern is that there are alignment parameters specific to each pipeline that might cause issues for the other pipelines.
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tjbencomo
Hi,
I'm trying to profile fusions, mutations, and expression from RNA-Seq data using programs from the CTAT pipeline. For consistency I thought it would be optimal to have a single BAM for each sample that can be run through each program (STAR-Fusion, CTAT Mutation pipeline, RSEM or Salmon).
I see that
ctat-mutationsand STAR-Fusion by default both use FASTQs as input and output BAM files, although both pipelines can use BAM files as input. Does it make sense to run one pipeline first and then use the output BAM file for the other programs? For example, I could run STAR-Fusion using the FASTQ files and then use the resulting BAM as input to the mutation calling pipeline and RSEM. Is there an alternative ordering that would be better? My concern is that there are alignment parameters specific to each pipeline that might cause issues for the other pipelines.