Bowtie indexes for custom reference genome

Question

[f.rivello]

Hi all,

I want to make my own bowtie indexes to align the sequences to a custom reference genome.

Is it necessary only to create a fasta file and then bowtie-build to have proper indexes for mapping or I should also create a GTF file? If so, how do you create a GTF file?

Thank you for youe help

[f.rivello]

Thank you. A GTF file not necessary to buid a custom bowtie index, but only a fasta file with my sequences right?

Sorry for the question, I am a beginner in the field.

[waqaskhokhar999]

yes we don't need gtf file to build genome index. Good luck

[ATpoint]

Bowtie is a DNA-seq aligner, not a splice-aware RNA-seq aligner. Therefore, it does not even has an option to accept a GTF. All you need is a fasta of the reference genome. Splice-aware aligners need information about splice and exon positions, that is why these files are necessary for e.g. tophat, hisat, star etc.

Answer 1

[waqaskhokhar999]

Bowtie can index from a set of DNA sequences. It produces six file which constitute the index. For more details please check this link manual section on index building