Question: How many index files will be generated from hisat2-build
0
gravatar for Xiaokang ZH
13 months ago by
Xiaokang ZH40
Xiaokang ZH40 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 • 895 views
ADD COMMENTlink modified 10 months ago by sxm8911140 • written 13 months ago by Xiaokang ZH40
1

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

ADD REPLYlink written 13 months ago by genomax52k

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

ADD REPLYlink written 13 months ago by Xiaokang ZH40
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 13 months ago by WouterDeCoster30k

No one ever said documentation was good in bioinfo :P

ADD REPLYlink written 13 months ago by Devon Ryan81k

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

have you solved the problem?

ADD REPLYlink written 10 months ago by sxm8911140
1

8 files is the expected output of indexing.

ADD REPLYlink written 9 months ago by WouterDeCoster30k
5
gravatar for Devon Ryan
13 months ago by
Devon Ryan81k
Freiburg, Germany
Devon Ryan81k wrote:

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

ADD COMMENTlink written 13 months ago by Devon Ryan81k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 878 users visited in the last hour