Question: my hisat cannot build index fileds normaly
gravatar for sxm891114
27 days ago by
sxm8911140 wrote:


I used this command: hisat2-build -f genome.fa -p 4 genome

then I got 8 index files. Theoretically, there're 8 file named genome.1.ht2 to genome.8.ht2

but my output had .1.ht2 .2.ht2 .3.ht2 .4.ht2 .7.ht2 .8.ht2 and

lack of genome.5.ht2/.6.ht2 but 2 extra

could you give me some help about that?

many thanks

rna-seq hisat • 140 views
ADD COMMENTlink written 27 days ago by sxm8911140
gravatar for genomax
27 days ago by
United States
genomax34k wrote:

As long as there was no error and you had 8 files you should be all set (A: How many index files will be generated from hisat2-build ). Move on to the mapping step.

ADD COMMENTlink modified 27 days ago • written 27 days ago by genomax34k

thanks. I don't know if I should re-name the two .sa file. I'll try to move on directly

ADD REPLYlink written 27 days ago by sxm8911140

You shouldn't rename them. The manual is unclear on the files created but there is nothing to worry about.

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ADD REPLYlink written 26 days ago by WouterDeCoster22k

Thanks, the problem has solved. I added a memory bank, then it worked normally


ADD REPLYlink written 26 days ago by sxm8911140
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