RSEM calculate-expression has only one sample in .isoforms.results file
Hello,
I think I have a few misunderstandings about how to use RSEM, and have provided my script below.
I have three questions:
- My script outputted a .isoform.results file, but with only one sample in it. As you can see from my script below, I call it on 4 samples. Was I supposed to run this script 4 times for each file?
- I call STAR aligner, but only see an output bam file. Why is there no .bai file?
- Is it correct to say that the line
/home/name/project/RSEM/AGP
tells RSEM the reference directory? If so, how did RSEM know where the index for star is? It is in the same directory, but it does not have the prefix “AGP”, as the prepare_reference script I previously ran only gave that prefix to the rsem files.
Thanks!
rsem-calculate-expression --star \
-p 64 \
/home/name/project/RSEM/rnaseq_rawfastq/01-dmsoR01_S1.fastq,/home/name/project/RSEM/rnaseq_rawfastq/02_dmsoR02.fastq,/home/name/project/RSEM/rnaseq_rawfastq/03_dmsoR03.fastq,/home/name/project/RSEM/rnaseq_rawfastq/04-DOXR01_S4.fastq,/home/name/project/RSEM/rnaseq_rawfastq/05-DOXR02_S5.fastq,/home/name/project/RSEM/rnaseq_rawfastq/06-DOXR03_S6.fastq \
/home/name/project/RSEM/AGP \
dmsovDox
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