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Old 11-05-2015, 10:59 PM   #1
zhanghao
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Default question about hisat2

I want to use hisat2. According to the manual, "Use extract_splice_sites.py (in the HISAT2 package) to extract splice sites from a GTF file", I do it as:
bac@bac-X10DAi:~/hisat2-2.0.0-beta$ python extract_splice_sites.py mus.gtf > s.txt

the mus.gtf is in the hisat2-2.0.0-beta folder, but the output s.txt is empty!!!

I do not know where is wrong???
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Old 11-06-2015, 03:45 AM   #2
GenoMax
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Are there any other errors? Does mus.gtf have content (i.e. it is not empty)?
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Old 11-07-2015, 12:05 AM   #3
zhanghao
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Quote:
Originally Posted by GenoMax View Post
Are there any other errors? Does mus.gtf have content (i.e. it is not empty)?
You are right, it seems the mus.gtf lack something. I just download this gtf file from ensembl at random. I try other gtf files, they are all ok!

But I found an another problem. When I run hisat2-build to index the genome, if I add --ss and --exons parameters, it can not finish with an error "illlegal instruction (core dump)". Is this due to insufficient memory? If I don't add these parameters, it is ok.

Also, I want to know whether adding "--ss" and "--exon" will give us a better result? Is these parameter like -G xx.gtf in tophat? and let the software map reads to transcripts first?
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Old 11-16-2015, 05:29 PM   #4
texy34
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You have to put the --ss and --exon parameters, and --large-index if needed or desired, after the path to your genome sequence even though the online manual and command line help has them before it. Like this:

hisat2-build -p 16 Triticum_aestivum.IWGSC1.0+popseq.29.dna.genome.fa --large-index --ss wheat_splice_sites.txt --exon wheat_exons.txt Triticum_aestivum
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