1 answer
The script is throwing errors.
How do you expect us to help if you don't tell us what's going wrong?
I used the same commands given in the manual, with the BAM files I have,
software/RSEM-1.2.25/rsem-calculate-expression -p 8 --paired-end \
--bam \
--estimate-rspd \
--append-names \
--output-genome-bam \
exp/LPS_6h.bam \
ref/mouse_ref exp/LPS_6h
Error:
Warning: The SAM/BAM file declares less reference sequences (955) than RSEM knows (41078)! Please make sure that you aligned your reads against transcript sequences instead of genome. RSEM can not recognize reference sequence name 1!
"rsem-parse-alignments /home/user/data/RSEM/Rat /home/user/data/RSEM/Rat.temp/Rat /home/user/data/RSEM/Rat.stat/Rat /home/ec2-user/data/Rat/*.bam 3 -tag XM" failed! Plase check if you provide correct parameters/options for the pipeline!
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