Use normalised reads for HISAT2/Braker1
I want to use braker for gene prediction of a denovo genome assembly using RNAseq data. I have 21 RNAseq samples.
My question is, for aligning using HISAT2, is it ok to use the normalised reads (using trinity: coverage 50) or use all 21 RNAseq files separately?
Any suggestion would be appreciated. Thanks
• 1,383 views
•
link
written
by
ersgupta •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
GO enrichment of DEGs - DeNovo RNAseq
written by Sowmya Pulapet •
-
reference-guided denovo assembly
written by askari.arezou94 •
-
Reconstructing an incomplete transcript of interest
written by Emily Wasson •
-
Trinity DeNovo assembly and problems to map reads to it
written by luca.rugiu •
-
Differences between "gene prediction" vs. "transcript reconstruction"
written by ljason2020 •
-
DEGs from *genes.results or *isoforms.results
written by Bioin •
-
stringtie merged gtf doesn't give any gene expression columns
written by Biologist
-
htseq read count zero ?
written by cvu
-
problem in Abundance Estimation using RSEM
written by bilal.sarwar •
-
How can I know what genes each Trinity ID are ?
written by tiago211287
