Whippet.jl
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timbitz
Lightweight and Fast; RNA-seq quantification at the event-level
can Whippet detect exon skip events? it seems that CE (core exon) doesn't contain exon skip. Thank you!
Dear Team, In the user manual of Whippet it is stated the following regarding the generation of sam files: julia bin/whippet-quant.jl fwd_file.fastq.gz --sam > fwd_file.sam samtools view -bS fwd_file.sam >...
I've seen a few issues posted here that describe lots of alternative first and alternative last events. These could simply be due to a noisy reference gtf. SUPPA makes it...
Hello I run many fastq file, but several ones failed. here is one of the them, I run second time but it is still there. > Whippet v0.11 loading and...
Hi, Timbitz: I'm using "Whippet" to compare alternative splicing of different samples from RNAseq data. The idea to identify AS events from event-level is really brilliant. When I finished the...
I've run into an issue with the likely misclassification of the strandedness of certain splice junctions. I'm working with a strand-specific RNA-Seq library for A. thaliana and generated a BAM...
And if so, how is then the whippet-delta treating those unique events in some samples? Thanks for the fantastic tool, Jose
Hi, Generally indexing works fine. However I am frequently experiencing two bugs that might need attention: 1. when the source gtf file contains only one gene in the gene_id field,...
Hi,, Running whippet-quant.jl on single end sample didn't work. (It always worked well for paired end) `run julia /home/luco/soft/Whippet.jl-0.10.4/bin/whippet-quant.jl -x /home/luco/index_whippet/human/human_index_whippet_10.0.4 /home/luco/work/nrf2_rbm47/fastq/29_1.fastq.gz -o /home/luco/work/nrf2_rbm47/output/29` ``` ERROR: LoadError: InexactError() Stacktrace: [1]...
Quantification after creating an index supplemented with bam files produces NAs in evens of interest
Hi, I'm interested in quatifying the PSI of a 5' splice site in a particular gene. The event is not in my annotation, but I can see that it's used...
