Reference sequence for indica Rice Paired End reads assembly using HISAT2

Question

[sharadlko1]

I am working on RNA-Seq based analysis of an indica rice variety. For reference based assembly of Paired End reads using HISAT2, I found indicia rice sequences at Ensembl. But, I am not sure which file(s) among the listed files at ftp, I need to download for building the genome index using HISAT2. I am new to RNA-Seq and NGS data analysis. Help me.

[GenoMax]

You should get the top-level unmasked DNA sequence which is the primary assembly (example of human file name below).

  Toplevel sequences unmasked:
    Homo_sapiens.GRCh37.dna.toplevel.fa.gz

For reference based assembly of Paired End reads using HISAT2

You can't do assembly of sequences with HISAT2. It is only an aligner. If you are interested in assemblies then you would want to use a program like trinity.

That said have you considered using transcriptome of rice with a program like salmon ( https://combine-lab.github.io/salmon/ ) to speed the process up significantly?

[sharadlko1]

Thank you very much for your help in selecting the right file for the reference based assembly. You are right, that I cannot use HISAT2 for assembly. Actually, I meant to say, I am using HISAT2 for mapping of PE reads in order to assemble the transcripts using Stringtie. Thank you for introducing me to salmon for expression analysis.