Question: Do STAR genome index and RSEM reference need to be from same files?
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gravatar for prabin.dm
3 months ago by
prabin.dm30
prabin.dm30 wrote:

Hi, I am using STAR for read alignment. The STAR genome index was built on .gtf and .fa downloaded from UCSC genome browser.

Should I run rsem-prepare-reference on the same .gtf and .fa files ? Or I can have rsem reference built on gft and fasta files downloaed from different source ?

star rsem rna-seq • 261 views
ADD COMMENTlink modified 3 months ago by WouterDeCoster37k • written 3 months ago by prabin.dm30
0
gravatar for grant.hovhannisyan
3 months ago by
grant.hovhannisyan1.4k wrote:

In general its a bad idea to use different reference genomes and annotations, there is a very high chance of some downstream incompatibilities. So unless there is a very strong reason you have to use different files, you should go with the same ones.

ADD COMMENTlink written 3 months ago by grant.hovhannisyan1.4k
0
gravatar for WouterDeCoster
3 months ago by
Belgium
WouterDeCoster37k wrote:

For STAR you use the genome (DNA) and for RSEM you use the transcriptome (cDNA), however, you can also create an index for RSEM using the genome and a gtf of all transcripts.

ADD COMMENTlink written 3 months ago by WouterDeCoster37k
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