which genome sequence fasta file should be used for builindg bowtie2 index ?

Question

[Pei]

Hi all:

this is a simple quesion:

when building bowtie2 index for tophat2 analysis, which genome sequence file should I used:

ftp://ftp.ensembl.org/pub/release-83/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz

or

ftp://ftp.ensembl.org/pub/release-83/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz ?

(I think the primary assembly should be used.)

Thanks in advance!

Best,

[GenoMax]

Get a pre-built sequence/index/annotation bundle from iGenomes, if you can use it: http://support.illumina.com/sequencing/sequencing_software/igenome.html

Answer 1

[Devon Ryan]

We usually use the primary assembly, but as long as you don't include the haplotype alleles you should be fine.

[Pei]

Many thanks to you!