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STAR rmRep: How to build the Star Index using *.fa files from the RepBase database. #15

Closed geng-lee closed 3 years ago

geng-lee commented 4 years ago

How to build the Star Index using .fa files from the RepBase database. There’s no .gtf file in the RepBase that corresponds to a *.fa file, so I can’t build an index. Whether you can provide this part of the code and data files. My sample uses Mus Musculus. My email address : leegengck@163.com

STAR rmRep: Takes output from cutadapt round 2. Maps to human specific version of RepBase used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads.

juuinn commented 2 years ago

I have the same question. could you please help? my email address is xiejun1029@163.com.

byee4 commented 2 years ago

You don't need a corresponding GTF file for repeat elements, as far as I know the GTF file is mainly used for spliced alignments, and ultimately this step is used to filter out rRNA and other shorter repetitive sequences. I would ultimately consult the STAR manual, but for rRNA filtering, you probably won't need it.

FionaMoon commented 1 year ago

Yeah, I check the STAR manual. The parameter --sjdbGTFfile was described as following:

STAR will extract splice junctions from this file and use them to greatly improve accuracy of the mapping. While this is optional, and STAR can be run without annotations,using annotations is highly recommended whenever they are available.

Annotation files are not necessary for STAR index.