Question: Bowtie indexes for custom reference genome
0
gravatar for f.rivello
8 days ago by
f.rivello0
f.rivello0 wrote:

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

rna-seq next-gen • 65 views
ADD COMMENTlink modified 8 days ago • written 8 days ago by f.rivello0

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.

ADD REPLYlink written 8 days ago by f.rivello0

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

ADD REPLYlink written 8 days ago by waqaskhokhar99910

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.

ADD REPLYlink written 8 days ago by ATpoint9.3k
1
gravatar for waqaskhokhar999
8 days ago by
waqaskhokhar99910 wrote:

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

ADD COMMENTlink written 8 days ago by waqaskhokhar99910
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