RSEM versus STAR/RSEM

[Jennifer Beane]

Hi,

I'm wondering if it is better to align with star within RSEM or to use STAR and --quantMode and feed the bam file to RSEM?  Does this produce equivalent results?

Thank you,

Jen

[Bo Li]

Hi Jen,

Here are the STAR parameters RSEM uses, it follows the ENCODE3 pipeline:

## ENCODE3 pipeline parameters
" --genomeDir $star_genome_path " .
' --outSAMunmapped Within ' .
' --outFilterType BySJout ' .
' --outSAMattributes NH HI AS NM MD ' .
' --outFilterMultimapNmax 20 ' .
' --outFilterMismatchNmax 999 ' .
' --outFilterMismatchNoverLmax 0.04 ' .
' --alignIntronMin 20 ' .
' --alignIntronMax 1000000 ' .
' --alignMatesGapMax 1000000 ' .
' --alignSJoverhangMin 8 ' .
' --alignSJDBoverhangMin 1 ' .
' --sjdbScore 1 ' .
" --runThreadN $nThreads " .
##

## different than ENCODE3 pipeline
## do not allow using shared memory
' --genomeLoad NoSharedMemory ' .
##

## different than ENCODE3 pipeline, which sorts output
BAM
## no need to do it here to save time and memory
' --outSAMtype BAM Unsorted ' .
##

## unlike ENCODE3, we don't output bedGraph files

' --quantMode TranscriptomeSAM '.
' --outSAMheaderHD \@HD VN:1.4 SO:unsorted '.

## define output file prefix
" --outFileNamePrefix $imdName ";
##



If you use the same parameter for STAR, you'll get the same results.

Best,
Bo

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[Malcolm Cook]

Thanks for supplying these defaults.

I read that --bam is deprecated in http://deweylab.github.io/RSEM/rsem-calculate-expression.html#DEPRECATED-OPTIONS

Does this mean that Jennifer's consideration to "use STAR and --quantMode and feed the bam file to RSEM" will someday no longer be possible?

Thanks,

~Malcolm Cook

[Colin Dewey]

Hi Malcom,

No, BAM support is not being removed.  This is simply a change in the way the options work.  Moving forward, you should use the "--alignments" option when providing an alignment file (in SAM, BAM, or CRAM format) as input.

Best,

Colin

[Malcolm Cook]

splendid news - thanks Colin...

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