Error in running RSEM

Question

[bioinformatics.queries]

Hi

I am trying to run RSEM and the command is as below

./rsem-calculate-expression --bowtie-path /home/shilpia2/bowtie2-2.3/ --phred64-quals -p 8 --output-genome-bam /data/shilpia2/NOR.sequecnes/293T/293TInput2_S21_L008_R1_001.fastq /data/shilpia2/ref/human /output/293T

However it shows the following error.

rsem-parse-alignments /data/ref/human 293T.temp/293T 293T.stat/293T 293T.temp/293T.bam 1 -tag XM The SAM/BAM file declares less than one reference sequence! "rsem-parse-alignments /shilpia2/ref/human 293T.temp/293T 293T.stat/293T 293T.temp/293T.bam 1 -tag XM" failed! Plase check if you provide correct parameters/options for the pipeline!

I have no clue as to how to debug it. Any help would be appreciated

Answer 1

[Qiongyi]

You should use "--bowtie2-path" rather than "--bowtie-path"

[bioinformatics.queries]

Thank you so much for your response.