Need help to do single denovo assembly with multiple RNA seq data
I have illumina RNA seq data from different tissues of one plant. Is it possible to do single assembly using all this RNA seq data from different tissues of one plant? Do I need to combine this libraries before assembly or is there any option in assembly tools itself?
Thank you
• 1,545 views
•
link
updated
by
Kristoffer Vitting-Seerup
•
written
by
ashokkumar.mb •
•
written
by
ashokkumar.mb •
1 answer
If you have a refrence genome tools such as Cufflinks or StringTie will work better - I have a small section in my vignette describing this here.
• 0 views
•
link
written
by
Kristoffer Vitting-Seerup
Log in to answer this question.
More posts like this
-
Allele specific expression of imprinted gens from 10x scRNA-seq data
written by singcell •
-
Re-analysis of multiple scRNAseq data
written by SG •
-
How to combining the RNA-seq data from different tissues of one individuals plant
written by yahalashinnosuke •
-
How to calculate RNA-seq read coverage around STOP codons
written by supertech
-
Trinity RSEM TMM matrix
written by ysbaek •
-
Forum: How to know that our trinity denovo assembly is good or not?
written by ashokkumar.mb •
-
Need help to separate a genome in different x coverage
written by ashokkumar.mb •
-
SRA data sets and runs
written by MAPK
-
Transcriptome hybrid assembly 454 + Illumina
written by giorgiocasaburi
-
Combining Data Of Multiple Vcfs Into One.
written by Sheila
Yes. Take a look at Trinity.
Depending on the amount of your data RAM requirements can be high but it is a well accepted option for eukaryotic transctiptome assembly.
Hey thank you so much, Found command for that
May I ask which command is that? I have the same question , need to combine different tissue RNAseq data of one plant. Thank you!