RNA-Seq plants
Hi all,
I am working with Barley plant and I have to do transcriptome analysis. I would like to look for differential gene expressions in treatment vs control. I am a little confused as which genome I should use for mapping. I will use STAR generating genome indexes. pseudomolecules_assembly.dna.toplevel.fa.gz or pseudomolecules_assembly.dna_sm.toplevel.fa.gz ?
https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-55/plants/fasta/hordeum_vulgare/dna/
Also what annotations are good, GTF or GFF ?
Thank you.
• 877 views
•
link
updated
by
jv
•
written
by
umeshtanwar2 •
•
written
by
umeshtanwar2 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Convert two Haplotypes into diploid genome assembly
written by Yiyi •
-
Help with choosing a model species for Augustus for a de novo assembled genome.
written by Vijith •
-
Index with unmasked or masked in HISAT2
written by san96 •
-
Which Fasta file and GTF file to use in STAR alignment
written by peru •
-
Hyb to analyze CLASH data?
written by divya.nandakumar •
-
DESeq2: Differential gene expression
written by umeshtanwar2 •
-
RNA-Seq Differential gene expression
written by umeshtanwar2 •
-
RNA-Seq Differential gene expression
written by umeshtanwar2 •
-
Transcriptome analysis for differential gene expression
written by umeshtanwar2 •
-
STAR for Genome Index and Alignment
written by umeshtanwar2 •
There should be any difference in the information provided in a GFF versus a GTF - these two file type only differ in subtle format differences. That said, building an index with STAR uses a GTF file.