rsem-prepare-reference generate a chain file to liftover the SNP of Transcriptome to genome? - Githubissues

deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

http://deweylab.biostat.wisc.edu/rsem/

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rsem-prepare-reference generate a chain file to liftover the SNP of Transcriptome to genome? #74

Closed wangyugui closed 7 years ago

wangyugui commented 7 years ago

Hi.

Can rsem-prepare-reference generate a chain file to liftover the SNP of transcriptome to genome?

We need this because mapping to transcriptome is more stable than mapping to genome.

wangyugui commented 7 years ago

gff3ToGenePred/genePredToFakePsl/pslToChain can do this job.