Question: Problems to index reference genome and to align RNAseq
0
gravatar for silas008
2.6 years ago by
silas00880
Brazil
silas00880 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 • 848 views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by silas00880
3
gravatar for Brian Bushnell
2.6 years ago by
Walnut Creek, USA
Brian Bushnell16k wrote:

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

ADD COMMENTlink written 2.6 years ago by Brian Bushnell16k
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