Hi,
I'd like to estimate gene and isoform expression levels from RNA-Seq data with RSEM.
Can it work alone (rsem-prepare-reference and rsem-calculate-expression) or does it need to be associated with the STAR aligner? in other words do I have first to produce bam files with STAR ans then perform a rsem-calculate-expression?
Thanks!
It needs STAR. You don't need to generate bam from STAR separately. Use rsem-prepare-reference to create index files for STAR. For example :
rsem-prepare-reference --gtf mm9.gtf --star --star-path /sw/STAR -p 8 /data/mm9 (genome file path) /ref/mouse_0 (output index files path with reference name)
You can build indices for bowtie/bowtie2/star/hisat2.
After preparing indices you can use rsem-calculate-expression.
You can also create the bam with STAR and then give it to rsem-calculate-expression to generate expression files. Follow these tutorials for more details :
http://deweylab.github.io/RSEM/README.html
https://github.com/bli25broad/RSEM_tutorial
You can use STAR alone to generate the bam files and pass them to rsem-calculate-expression by adding --bam to let it know the input is bam alignment file instead of reads.
In another word, if you choose RSEM, it can start from index preparation using rsem-prepare-reference and then use rsem-calculate-expression and add --star to use STAR to align the reads and generate the downstream analysis file.
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