Is it correct cammand for hisat indexing

Question

[Bioinfonext]

/home/yog/software/hisat2-2.0.0-beta/hisat2-build -c Rs_1.0.chromosomes.fix.fasta Radish_index -p 8 --ss radish_splice --exon radish_exon

Where fasta is genome file

Radish_index is index base name

[WouterDeCoster]

Offtopic comment: what you mean is "command" instead of "cammand". I've tried to hint that in a few previous threads, but you probably missed it.

Ontopic comment: how to create a hisat index is clearly explained in the manual.

Slightlty offtpic comment: you are using an outdated version of hisat2

[Bioinfonext]

Thanks for right suggest. trying to switch to latest version.

Answer 1

[Satyajeet Khare]

Small correction. You can remove -c

/home/yog/software/hisat2-2.0.0-beta/hisat2-build Rs_1.0.chromosomes.fix.fasta Radish_index -p 8 --ss radish_splice --exon radish_exon

Also, you may want to try without --ss and --exon options as these options will need large RAM.

[Bioinfonext]

Error while running Hisat2:

[root@psgl hisat2]# /home/yog/software/hisat2-2.0.0-beta/hisat2 -p 8 -x Radish_index -1 /data/SNU_work/Analysis/unmapped/unmapped/unmapped_R1.fq -2 /data/SNU_work/Analysis/unmapped/unmapped/unmapped_R2.fq --max-intronlen 200079

(ERR): hisat2-align died with signal 11 (SEGV) (core dumped)

[Satyajeet Khare]

Can you try without --max-intronlen parameter?

How was your index? Did hisat2-build run without error? If the issue persists, can you build index again and try alignment?

Also, though not at the time of indexing, you can provide --ss at the time of alignment such as...

hisat2 -p 10 --ss splicesites.txt -x genome_index -1 R1.fastq -2 R2.fastq

hisat2 -p 10 --known-splicesite-infile splicesites.txt -x genome_index -1 R1.fastq -2 R2.fastq

[Bioinfonext]

I want to install latest version of hisat2. I am confused between binary and source files:

Do I need to download both:

ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.0.5-source.zip

ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.0.5-Linux_x86_64.zip

And after unzip what should I do?

[Bioinfonext]

Thanks ...I installed the latest version and now it running well.