Question: How many index files will be generated from hisat2-build
0
gravatar for Xiaokang ZH
4 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 • 338 views
ADD COMMENTlink modified 24 days ago by sxm8911140 • written 4 months ago by Xiaokang ZH20
1

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

ADD REPLYlink written 4 months ago by genomax34k

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

ADD REPLYlink written 4 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 4 months ago by WouterDeCoster22k

No one ever said documentation was good in bioinfo :P

ADD REPLYlink written 4 months ago by Devon Ryan71k

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

have you solved the problem?

ADD REPLYlink written 24 days ago by sxm8911140

8 files is the expected output of indexing.

ADD REPLYlink written 24 days ago by WouterDeCoster22k
4
gravatar for Devon Ryan
4 months ago by
Devon Ryan71k
Freiburg, Germany
Devon Ryan71k wrote:

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

ADD COMMENTlink written 4 months ago by Devon Ryan71k
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: 1283 users visited in the last hour