Problems to index reference genome and to align RNAseq
I'm trying to align RNAseq data with STAR aligner. The reference genome for mice is split in 1-22 + X,Y and MT.
Should I create the reference genome index with splited chromosome or should I use a merged fasta file containing all of the individual chromosomes?
If I have indexed splited chromosomes, when I align the reads, should I do that on separated chromosomes or on merged fasta file?
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Index and map using a single fasta file containing all reference sequences.
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Brian Bushnell
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