Estimating Transcript Abundance with RSEM
Dear All
I would like to run Estimating Transcript Abundance for a dataset using RSEM.
By referring to the link below, it mentioned
if alignment_based est_method:
--aln_method <string> bowtie|bowtie2|(path to bam file) alignment method. (note: RSEM requires bowtie)
(if you already have a bam file, you can use it here instead of rerunning bowtie)
Since I already run bowtie2 for this sample before, I would like to use the bam file for this sample instead of rerun.
May I know how to write path to bam file?
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srhhaines9 •
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wes •
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wes •
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You mention a link in your question, but there doesn't appear to be a link. How did you run bowtie2? RSEM requires that you aligned to the genome rather than to the transcriptome.
This is the link.
https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification
For bowtie2 run, the script is following the link below https://github.com/trinityrnaseq/trinityrnaseq/wiki/RNA-Seq-Read-Representation-by-Trinity-Assembly
My guess would be you do
--aln_method=bowtie2_TB2.bam, but i've never quantitated using RSEM via trinity before. It you are finding it confusing, it might be worth using RSEM directly.I was unable to make this work. Has anyone had any success calling a previously created .bam file using --aln_method command?