Question: Build a HISAT2 index of hg 19
0
gravatar for mlemusfuentes
6 months ago by
mlemusfuentes10 wrote:

hello everyone, I'm new with regards to RNA-Seq analysis, I'm learning to use HISAT2. My question is relates with the step of build index. the command line are the following according to nprot2006:

$ extract_splice_sites.py hg19_data/genes/hg19.gtf >hg19.ss (ready)

$ extract_exons.py hg19_data/genes/hg19.gtf >hg19.exon (ready)

but when I was running the second part:

hisat2-build --ss hg19.ss --exon chrX.exon hg19_data/genome/hg19.fa hg19_tran (it is not ready)

it reached to generate seven files with the follows names:

hg19_tran.1.ht2; hg19_tran.2.ht2; hg19_tran.3.ht2; hg19_tran.4.ht2; hg19_tran.7.ht2; hg19_tran.8.ht2; hg19_tran.rf

the problem: last friday there was a blackout power supply and with this the computer was turned off before finishing.

My question: does anyone know how much files will be generated in the build index?, if a file could be generated, can It be run only the one I'm missing?

I will be attentive to your comments

thanks you all.

rna-seq • 446 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by mlemusfuentes10
1

If there was a computer crash during the building of the index you should start over at hisat2-build step (delete those *.ht2 files) .. just to be safe.

ADD REPLYlink modified 6 months ago • written 6 months ago by genomax59k
1

you say that all working was lost?, delete those *.ht2 would be like starting over...

ADD REPLYlink written 6 months ago by mlemusfuentes10

At the index build step, unfortunately yes, since I don't think there is any way for the program to pickup from where things went down.

ADD REPLYlink modified 6 months ago • written 6 months ago by genomax59k
1

or you can download index for hg19 from hisat2 group website (for genome. only primary assembly): ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/hg19.tar.gz

ADD REPLYlink written 6 months ago by cpad011210k

Where can I get its corresponding FASTA reference sequence and the annotation file?

ADD REPLYlink written 5 months ago by ag1805x110

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ (chromFa.tar.gz) and gtf/gff3 from UCSC table browser

ADD REPLYlink modified 5 months ago • written 5 months ago by cpad011210k
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