Question: Hisat2 alignment error
1
gravatar for blooming.daisy333
3 months ago by
blooming.daisy33310 wrote:

Hi all,

Im using Hisat2 to align RNAseq data and encountering following error:

(ERR): hisat2-align died with signal 8 (FPE) (core dumped)

using following command

./hisat2 --mp 0,0 --np 0 --pen-noncansplice 10000000 --min-intronlen 20 --max-intronlen 10000 --novel-splicesite-outfile /data/memona/hisat2-2.1.0/result/ --rna-strandness RF --dta -p64 --summary-file -x /data/memona/hisat2-2.1.0/hisat_index -1 /data/memona/Trimmomatic-0.36/SRR9591_E_1P.fq -2 /data/memona/Trimmomatic-0.36/SRR9591_E_2P.fq -S /data/memona/hisat2-2.1.0/result/hisat_align.sam

can anyone kindly suggest possible cause and solution to the problem.

Thanks

next-gen • 137 views
ADD COMMENTlink modified 3 months ago by Vijay Lakhujani3.0k • written 3 months ago by blooming.daisy33310
1
gravatar for Vijay Lakhujani
3 months ago by
Vijay Lakhujani3.0k
India
Vijay Lakhujani3.0k wrote:

Looks like these issues have been already taken care in the recent version. Check your HISAT version using

hisat2 --version

Update if necessary

ADD COMMENTlink written 3 months ago by Vijay Lakhujani3.0k

im using hisat2-2.1.0 version.

i have resolved the above problem after correcting one filter but now problem is that im unable to get information about splice junctions with this command. its producing only alignment and nothing else. any kind help???

thank you

ADD REPLYlink written 3 months ago by blooming.daisy33310

Could you try changing this

--novel-splicesite-outfile /data/memona/hisat2-2.1.0/result/

to

--novel-splicesite-outfile /data/memona/hisat2-2.1.0/result/novel.sites.txt
ADD REPLYlink written 3 months ago by Vijay Lakhujani3.0k

thanks for the guidance. yes it has produced the output but is giving only 3 fields given below:;

chr1    329728  329839  -
chr1    330066  330757  -
chr1    581256  581357  +

while not mentioning the canonical/non canonical status and junction nucleotide info.

further is it important to build the index with --ss and --exon options to determine the splice sites...????

ADD REPLYlink written 3 months ago by blooming.daisy33310
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