We are currently processing our RNA-Seq datasets using the Illumina DRAGEN pipeline, which outputs high-quality splice junction tables (SJ.out.tab / *.SJ_as_VCF.tsv files) along with standard BAM/CRAM files.
Questions: Can the DROP splicing pipeline / FRASER2 directly parse and ingest Illumina DRAGEN SJ.out.tab files as a starting count matrix to bypass the computationally expensive splitread counting step?
If using DRAGEN SJ.out.tab tables is supported or possible with minor parsing, what do the DROP maintainers recommend regarding filtering? And would it impact other steps in the FRASER2 pipeline?
We are currently processing our RNA-Seq datasets using the Illumina DRAGEN pipeline, which outputs high-quality splice junction tables (SJ.out.tab / *.SJ_as_VCF.tsv files) along with standard BAM/CRAM files.
Questions: Can the DROP splicing pipeline / FRASER2 directly parse and ingest Illumina DRAGEN SJ.out.tab files as a starting count matrix to bypass the computationally expensive splitread counting step?
If using DRAGEN SJ.out.tab tables is supported or possible with minor parsing, what do the DROP maintainers recommend regarding filtering? And would it impact other steps in the FRASER2 pipeline?