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 ?
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written
by
prabin.dm
2 answers
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.
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.
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