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deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
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Running with strandedness fails on rsem-tbam2gbam to produce output-genome bam #148

Open akmorrow13 opened 3 years ago

akmorrow13 commented 3 years ago

Hello,

I am running RSEM with --paired-end and --strandedness reverse. However, rsem-tbam2gbam fails with error Detected partial alignments for read XXX, which RSEM currently does not support! Is is possible to convert the transcript bam files to the genome bam file when strandedness is set?

RSEM version: 1.3.3 Command run: rsem-calculate-expression --num-threads 4 --bowtie2 --sampling-for-bam --output-genome-bam --sort-bam-by-coordinate --sort-bam-memory-per-thread 1G --estimate-rspd --paired-end 1.Ptrim.fastq 2.Ptrim.fastq GRCh38_rsem rsem_output