Question: Do I have to use index with trans information for RNA-seq alignment by Hisat2?
0
gravatar for ben.kunfang
6 days ago by
ben.kunfang10
ben.kunfang10 wrote:

Hi,

I am a newbie in RNA-seq analysis. I would like to use HISAT2 for RNA-seq alignment. In HISAT2 website, I found that pre-built index have genome_snp_tran of grcm38 and genome of mm10. I was wondering if I could use mm10 genome for RNA-seq alignment? If I cannot, I was wondering how can build an index for mm10 RNA-seq alignment. Thanks!

Best, Kun

hisat2 rna-seq • 81 views
ADD COMMENTlink modified 6 days ago by Istvan Albert ♦♦ 83k • written 6 days ago by ben.kunfang10
1
gravatar for Istvan Albert
6 days ago by
Istvan Albert ♦♦ 83k
University Park, USA
Istvan Albert ♦♦ 83k wrote:

HISAT2 was designed to align transcriptomic reads to genomes, thus you can use the genome file.

ADD COMMENTlink written 6 days ago by Istvan Albert ♦♦ 83k

Thanks a lot! In this case, I can directly use the pre-built mm10 index for RNA-seq alignment without trans in it, right? If you don't mind, can I ask why hisat2 offers the trans and snp index for grcm38 if it can handle the transcriptomic alignment by itself? Thanks again!

ADD REPLYlink written 6 days ago by ben.kunfang10

The tool can align against transcriptomes as well, but in those cases, one would not be able to detect a new splice variant and most pipelines would work differently.

ADD REPLYlink written 6 days ago by Istvan Albert ♦♦ 83k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1041 users visited in the last hour