Question: Can I use RSEM to deal with tophat output bam files?
2
gravatar for gyoubing
4.3 years ago by
gyoubing20
China
gyoubing20 wrote:

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 !

rsem rna-seq tophat • 2.9k views
ADD COMMENTlink modified 2.5 years ago by fu_entomology20 • written 4.3 years ago by gyoubing20
1
gravatar for Devon Ryan
4.3 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

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.
 

ADD COMMENTlink written 4.3 years ago by Devon Ryan88k

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

Best wishes!

ADD REPLYlink written 4.3 years ago by gyoubing20
1
gravatar for fu_entomology
2.5 years ago by
United States
fu_entomology20 wrote:

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

ADD COMMENTlink written 2.5 years ago by fu_entomology20
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