single-cell-prior is not giving me any values

deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

http://deweylab.biostat.wisc.edu/rsem/

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single-cell-prior is not giving me any values #196

Open TdzBAS opened 1 year ago

TdzBAS commented 1 year ago

when I use the following command, I only get 0 values for the new pme columns in my isoforms.results. Input data is a single cell dataset. How can this be?

rsem-calculate-expression --paired-end --star --no-bam-output --estimate-rspd --star-gzipped-read-file --single-cell-prior --calc-pme ${filename1} ${filename2} Simulation/ref/reference files/SRR23209435

Thanks!

TdzBAS commented 1 year ago

Update: I solved it. Somehow one gets no pme values if you use the zipped input fastq files. I had to unzip them and provide the unzipeed read in file and it calculated the pmes.

Best Tolga