Question: Problems to index reference genome and to align RNAseq
gravatar for silas008
4.3 years ago by
silas008140 wrote:

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?

chromosome index rnaseq • 1.2k views
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by silas008140
gravatar for Brian Bushnell
4.3 years ago by
Walnut Creek, USA
Brian Bushnell17k wrote:

Index and map using a single fasta file containing all reference sequences.

ADD COMMENTlink written 4.3 years ago by Brian Bushnell17k
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