Hello everyone, I have a question about genome indexing with STAR. As you all known STAR requires lots of memory for indexing. I have 32 GB RAM on my computer. I want to use some RNA-Seq data for alternative splicing analysis using DEXSeq, ASPli etc. As I know the aligner must be splice-aware and I decided to use STAR.
I indexed hg38 with STAR without using --sjdbGTFfile parameter and it worked. But as I know to create index with splice junction information I need that parameter. When I use it with hg38.knownGene.gtf from Ensembl, STAR indexing is killed.
Is there any way to create splice junction information to indexed genome in STAR? Or as another option can I use hisat2 for the same purpose?
Thank you in advance.
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