Question: which genome sequence fasta file should be used for builindg bowtie2 index ?
2
gravatar for lin.pei26
3.4 years ago by
lin.pei2690
China
lin.pei2690 wrote:

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 • 809 views
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by lin.pei2690

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

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by genomax69k
1
gravatar for Devon Ryan
3.4 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

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

ADD COMMENTlink written 3.4 years ago by Devon Ryan91k
0
gravatar for lin.pei26
3.4 years ago by
lin.pei2690
China
lin.pei2690 wrote:

Many thanks to you!

 

ADD COMMENTlink written 3.4 years ago by lin.pei2690
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