At beginning I was using Tophat-Cufflinks and had processed several sets of data. But it was way too slow so I switched to STAR. However, I found that output from STAR has much less number of isoform detected than Tophat-Cufflinks. Also the output from STAR seems to be all annotated. So I wonder if there is an option for STAR to identify new splicing sites.
•
written
by
zhangzhenyusz •
1 answer
As this was very difficult to find (like googling for STAR novel splice), I will post it here so others can benefit. From (one of) STAR paper:
In addition to detecting annotated and novel splice junctions, STAR is capable of discovering more complex RNA sequence arrangements, such as chimeric and circular RNA.
P.S.: read section 8) 2-pass mapping from STAR manual.
Log in to answer this question.
-
Different annotations for different isoforms from the same gene
written by Chikae •
-
cuffdiff not performing tss, CDS-level transcription difference, splicing, promoter preference and …
written by cuijinjincui4 •
-
Why does cuffdiff test differential isoform expression for genes with only one annotated transcript?
written by unsupervised_learner •
-
running Cufflinks with input from HIsat2
written by dovah •
-
Cufflinks with STAR BAM and Tophat BAM produces different results
written by RT •
-
mapping RNAseq reads to a genbank isoforme that is not in Reference Annotation
written by fta.mirzadeh •
-
From Cuffdiff Output to CummeRbund analysis/visualisation
written by Wet&DryImmunology
-
Cuffdiff (weird) output
written by rna-seq_researcher •
-
Bacterial RNAseq transcription start sites
written by D.a.forrest •
-
Cufflinks & Cuffdiff Novel Isoform Detection
written by andrew.j.skelton73
