Merging stringtie assemblies using stringtie merge
I have a set of 2 transcriptome samples
Sample1 - A. control B. treated
Sample2 - A. control B. treated
I assembled the transcriptome using stringtie
Objective is to compare A vs B for sample1 and A vs B for sample2.
How should I merge the assemblies using stringtie --merge ?
Should I merge assemblies separately for sample 1 and sample 2 or both of them together?
i.e. while running stringtie --merge, should I run in twice; once with a mergelist.txt file for sample1 and then for sample2.
• 3,869 views
•
link
written
by
lakhujanivijay
1 answer
This depends on your hypothesis, but the idea generally is to merge all assembled transcriptomes, so that you have an "experiment-wide transcriptome", rather than stratifying.
• 0 views
•
link
written
by
andrew.j.skelton73
Log in to answer this question.
More posts like this
-
How do I bin my individually assembled metagenome samples
written by prateekshettys •
-
Metagenome binning of samples with individual assembly.
written by jylee •
-
DeSeq design
written by chimerajit •
-
RNAseq data for Deseq2 from different library
written by luckysardar171 •
-
Stringtie Error: Getting the input alignment file is not sorted! even though file is sorted
written by venura
-
Unequal sample sizes Deseq2
written by Payal
-
Differential Expression in DEseq2 to GSEA (9 samples, 3 conditions)
written by bryce.kirby •
-
StringTie final sample gtf
written by samuel
-
DESeq2 Normalization of time course
written by EVR
-
Can't group samples in StringTie for differential expression
written by CandiceChuDVM
