Can I use RSEM to deal with tophat output bam files?

Question

[gyoubing]

I want to use Trinity's Differentially Expressed Analysis pipeline to analysis my RNA-seq Data--reads mapped to reference genome with Tophat.

But I'm not sure that Can I use RSEM to deal with topaht output bam files? Or just only to use HT-seq?

Many Thanks!

Answer 1

[Devon Ryan]

RSEM is meant to work with alignments to the transcriptome. Unless you can get tophat to do that (even if you map against the transcriptome, the output will be genomic mappings), then don't use the results with RSEM.

[gyoubing]

Thanks a lot. Your answer is very helpful for me!

Best wishes!

Answer 2

[fu_entomology]

Well, Devon Ryan is right about RSEM.

However, I was just reading their tutorial, it seems like there is a way to extract transcripts sequences from genome. Of course you will have to have a genome fasta file and a gtf/gff file to run RSEM as below:

gunzip ref/Mus_musculus.GRCm38.dna.toplevel.fa.gz
gunzip ref/Mus_musculus.GRCm38.82.chr.gtf.gz
software/RSEM-1.2.25/rsem-prepare-reference --gtf ref/Mus_musculus.GRCm38.82.chr.gtf \
                       --bowtie2 --bowtie2-path software/bowtie2-2.2.6 \
                       ref/Mus_musculus.GRCm38.dna.toplevel.fa ref/mouse_ref

The full tutorial is here: https://github.com/bli25ucb/RSEM_tutorial