Question: my hisat cannot build index fileds normaly
0
gravatar for sxm891114
6 months ago by
sxm8911140
sxm8911140 wrote:

hello,

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 .2.sa .3.sa

lack of genome.5.ht2/.6.ht2 but 2 extra genome.2.sa/.3.sa

could you give me some help about that?

many thanks

rna-seq hisat • 339 views
ADD COMMENTlink written 6 months ago by sxm8911140
2
gravatar for genomax
6 months ago by
genomax46k
United States
genomax46k 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 6 months ago • written 6 months ago by genomax46k

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

ADD REPLYlink written 6 months ago by sxm8911140
1

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 6 months ago by WouterDeCoster27k

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

T_T

ADD REPLYlink written 6 months ago by sxm8911140
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