Differential Expression Analysis

[gringer]

Use supertranscripts as your reference genome:

https://github.com/Oshlack/Lace/wiki

https://github.com/trinityrnaseq/trinityrnaseq/wiki/SuperTranscripts

[ASintsova]

I don't know much about plants, but it sounds like you might want to try to build de novo transcriptome assembly - https://www.sciencedirect.com/scienc...14662817301032

[DeDeoxys]

I am working with novel RNAseq data from a type of grass whose genome has not yet been completely sequenced or annotated. I have a number of FASTQ files with RNAseq data from different parts of the plant and am trying to conduct a differential expression analysis of these files. I was planning to use the DEGseq package in R to conduct the analysis, but from what I understand, this requires me to map the reads to an index to ultimately convert them to the .bed format and I would also need a reference genome file in the ucsc refFlat format. Since this plant genome has not even been sequenced, these files are unavailable, so I thought to map the reads to the genome of brachypodium distachyon, which is a model organism for grasses. I was able to create an index through bowtie using the genome from phytozome, but I have not been able to find a reference file for brachypodium in the reFlat or GTF format. Is there any way to convert to or create a reference file in the GTF or refFlat format, and am I even on the right track to conduct differential expression analysis on these files?
I also have access to the original RNA assembly data which came from an illumina HiSeq. I'm not sure if this would be helpful.