Question: hisat2-build index problems for C. elegans genome
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gravatar for mltm.isik
4.7 years ago by
mltm.isik0
mltm.isik0 wrote:

I'm trying to build an index for C. elegans genome using the command below:

$HISAT2_HOME/hisat2-build Caenorhabditis_elegans.WBcel235.dna.toplevel.fa -ss splice_sites.txt and --exon exon.txt C_elegans

It builds an index in under 2 minutes but when I use hisat2 inspect --ss --exon C_elegans, I see that splice sites and exon info is not included in the index. Should I add other options to the script for this to work?

head splice_sites.txt

I 4357 5194 -
I 5295 6036 -
I 6326 9726 -
I 9845 10094 -
I 10584 11617 +
I 11556 11617 +
I 11560 11617 +
I 11560 11622 +
I 11685 14949 +
I 11688 14950 +

head exons.txt
I 3746 3908 -
I 4118 4357 -
I 5194 5295 -
I 6036 6326 -
I 9726 9845 -
I 10094 10229 -
I 10412 10584 +
I 11494 11560 +
I 11617 11688 +
I 14949 15159 +

ADD COMMENTlink written 4.7 years ago by mltm.isik0
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