Indexing a genome
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.
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rani1983 •
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jitendoshi2006 •
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jitendoshi2006 •
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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).
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what is the purpose of indexing a genome
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.
You can use the same bowtie2 commands supplied here for indexing the contigs as long as they are in fasta format.
You need to put your contigs in fasta format and then run bowtie2-build as example given by Mehmet .
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.