Bowtie2-Indexing and ....

Question

[Arash]

Hi

I have a question about Bowtie2 index. Can i use botiew2 index files that i provide in iGenome? The folders contain 6 files?which would be use for mapping?

Thanks

[WouterDeCoster]

Try to use a more informative title for your thread(s), e.g. "iGenome indexes for bowtie2"

Answer 1

[Medhat]

I would change the question to more informative one like,
Using Bowtie2 index for iGenome (just example)

and from the manual (I am not expert here) but I can read

**** iGENOME CONTENTS

---

Each iGenomes has the following nested directory structure:

• Species/
• Source/
• Build/
• Annotation/ Sequence/

...

Sequence/BowtieIndex/ contains an index of the whole genome for use with the Bowtie aligner, which is also used by TopHat/Cufflinks.

Sequence/Bowtie2Index/ contains an index of the whole genome for use with the Bowtie2 aligner, which is also used by TopHat2.

Sequence/BWAIndex/ contains an index of the whole genome for use with the BWA aligner. Since the BWA index scheme changed at version 0.6.0, both versions 0.5.x and 0.6.0 (and higher) are included.

so It means yes you can use it

regarding which file to use

bowtie2-build outputs a set of 6 files with suffixes .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, and .rev.2.bt2. In the case of a large index these suffixes will have a bt2l termination. These files together constitute the index: they are all that is needed to align reads to that reference.

They are all that is needed to align reads to that reference.

Based on which bowtie indexing you used you need to copy it into the destination mentioned upove,

before doing all of that make sure that you can not find your desired index in iGenomes

[Arash]

Thanks so much! Do have any information for Hisat2 indexing?

[Medhat]

very similar to bowtie

https://ccb.jhu.edu/software/hisat2/manual.shtml#the-hisat2-build-indexer

[GenoMax]

@Aarsh: Very similar but you would need to create a new index (I don't think iGenomes has HISAT2 indexes).

[Medhat]

I meant very similar in the way of creating it "the command and resulting files" :)