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

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,

rna-seq
• 2,282 views • link
updated by Ram Ram • written by Pei Pei

1 answer

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

• 0 views • link
written by Devon Ryan Devon Ryan

Many thanks to you!

• 0 views • link
updated by Ram Ram • written by Pei Pei

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