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How many index files will be generated from hisat2-build

When using hisat2-build, several files with .ht2 extension will be generated. And in my experiment, there are 8 files generated, with 6 files of big size, and the other 2 of small size. Is it always the case that 8 index files will be generated? Or how can I predict how many index files will be generated from hisat2-build?

rna-seq hisat2 index
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updated by Archit • Archit • written by Xiaokang • Xiaokang

Any particular reason you are worried about how many files are generated by this process?

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written by GenoMax GenoMax

No particular reason for now, just curious :) But may be useful in the future.

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written by Xiaokang • Xiaokang

The manual is a bit weird about this...:

hisat2-build outputs a set of 6 files with suffixes .1.ht2, .2.ht2, .3.ht2, .4.ht2, .5.ht2, .6.ht2, .7.ht2, and .8.ht2

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written by WouterDeCoster WouterDeCoster

No one ever said documentation was good in bioinfo :P

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written by Devon Ryan Devon Ryan

same to you. my output includ 6 .ht2 and 2 .sa file

have you solved the problem?

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written by sxm891114 • sxm891114

8 files is the expected output of indexing.

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written by WouterDeCoster WouterDeCoster

I noticed that there were more files being generated while the build was in progress, but most of them got deleted and I was left with 8. Is that normal? Because I don't know if they are supposed to get deleted .

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written by Archit • Archit

As long as there was no error during index generation you should be good to move forward.

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written by GenoMax GenoMax

1 answer

Yes, there are always 8 files that result from indexing.

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written by Devon Ryan Devon Ryan

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