HISAT2 rn6.gtf file

Question

[saj98]

Hello I am using Hisat2 to align RNAseq data. I downloaded Rn6 genome from the official web site of Hisat2. It is available on the right side. However, the package does not have gtf file. How I can process the command of $ stringtie -p 8 -G chrX_data/genes/chrX.gtf -o ERR188044_chrX.gtf –l ERR188044 ERR188044_chrX.bam ?

I appreciate your help Shaima

Answer 1

[h.mon]

Download the gtf from Ensembl:

ftp://ftp.ensembl.org/pub/release-90/gtf/rattus_norvegicus/

edit: I did not check the Rattus norvegicus index file, but I believe HISAT2 uses the Rattus_norvegicus.Rnor_6.0.90.gtf.gz to build the index. Check the script they used to build the index, it is bundled together in the same .gz.

[saj98]

Thank you so much, the link very useful. I have one quick question: which gtf extension I should download and use for stringtie? I appreciate your answer

[h.mon]

See my edited answer.

[saj98]

I build my index file, Thank you so much

[WouterDeCoster]

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