Need tools recommendation for plant RNAseq data

Question

[bioinforesearchquestions]

Hi,

I have RNA data from 10 samples of Cannabis plant. I am planning to do the following analyses with these samples

-) De novo Assembly (ex: Trinity, Velvet, SOAPdenovo, etc. Which is recommended for plants?)

-) Variant calling ( does GATK support plant variant calling?

-) Functional annotation like COG, GO, KEGG, swissprot, NR database (ex: BLAST2GO tool, any other recommendation)

-) Differential gene expression (DESEQ2 or EDGER or LIMMA, which one is recommended for plant dataset?)

[h.mon]

There is already a (partially) similar paper, look at its methods to draw some ideas. If you follow the paper methodology, upgrade the tools used (hisat - stringtie - ballgown onstead of tophat - cufflinks). There is a Cannabis genome, unfortunately, it seems it is not annotated.

Answer 1

[apeltzer]

First of all: What kind of data do you have? Is it short read data? Is it long reads (e.g. PacBio SMRT/Nanopore?).

• If you have short read data, try SOAPDenovo for assembly. In case you have long read data, I had pretty good experiences with "Canu".

For Variant calling I assume that GATK should work - but didn't use it on plant data yet.

• DESEQ2 should work fine, just make sure to use a proper reference genome when mapping reads and then annotate properly before doing the expression analysis.

[bioinforesearchquestions]

Plant RNASeq data, paired-end, 101 bp from Illumina platform.