Question: How many index files will be generated from hisat2-build
0
gravatar for Xiaokang ZH
6 months ago by
Xiaokang ZH20
Xiaokang ZH20 wrote:

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?

index rna-seq hisat2 • 477 views
ADD COMMENTlink modified 11 weeks ago by sxm8911140 • written 6 months ago by Xiaokang ZH20
1

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

ADD REPLYlink written 5 months ago by genomax39k

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

ADD REPLYlink written 5 months ago by Xiaokang ZH20
1

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

ADD REPLYlink written 5 months ago by WouterDeCoster24k

No one ever said documentation was good in bioinfo :P

ADD REPLYlink written 5 months ago by Devon Ryan74k

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

have you solved the problem?

ADD REPLYlink written 11 weeks ago by sxm8911140

8 files is the expected output of indexing.

ADD REPLYlink written 11 weeks ago by WouterDeCoster24k
4
gravatar for Devon Ryan
5 months ago by
Devon Ryan74k
Freiburg, Germany
Devon Ryan74k wrote:

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

ADD COMMENTlink written 5 months ago by Devon Ryan74k
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