Indexing a genome

Question

[jitendoshi2006]

What does indexing a genome mean? How to index a genome? I have CHO genome from chogenome.org. I want to index the genome since I would like to align my reads from NGS to the genome using Bowtie.

[GenoMax]

what is the purpose of indexing a genome

[rani1983]

Hi, I want to index the contigs of the genome to RNA seq reads. How to index the contigs in Bowtie and in what file format should i use the genome contigs for indexing? Please help with this query.

[Brian Bushnell]

Bowtie is not splice-aware and thus not appropriate for eukaryotic RNA-seq. You should use a splice-aware aligner such as STAR or BBMap.

[Sej Modha]

You can use the same bowtie2 commands supplied here for indexing the contigs as long as they are in fasta format.

[Titus]

You need to put your contigs in fasta format and then run bowtie2-build as example given by Mehmet .

Answer 1

[Mehmet]

Hi For bowtie2, you need to index a genome, thus the indexed genome will be ready for Tophat2 to run mapping. Bowtie2 will prepare index to make tophat job easy.

for indexing by bowtie2:

bowtie2-build genome.fa indexname

for tophat (alingning reads to genome);

in index name argument in tophat,

just write indexname (you created above).