Whippet.jl

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Question regarding relative proportion of TE events human transcriptome

10

Dear Team, I run Whippet on my paired-end, unstranded, polyA+ RNA-seq dataset. The dataset is of 75bp length (all reads in all samples have this length) and performed in triplicates...

JamalEH

Dear Tim, I would like to make an MA plot showing dPSI and gene/event expression relationships. In the PSI files there is a Total Reads column. Should I use the...

JamalEH

Hi, First I want to know the meaning of "Total Reads" in .psi.gz files. And what kind of analysis can we use this data to do? Second, I want to...

itszhengan

Merging bams for including novel splice sites makes a really big bam :(

11

Hi, I have about 30 samples which I want to do a differential splicing analysis on. The instructions for including unannotated splice sites suggests that I first merge all my...

aleighbrown

Novel events

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Is there a way to (easily) identify the novel events, or is it possibly to add a label to novel events in future updates?

KalynaLab

Creating annotation files

1

Hi, How were the annotation files for refseq created / where were they taken from? The transcript reference sequence identifiers lack veresion numbers and I would like to re-create the...

Peter-J-Freeman

Error on whippet-quant.jl

1

Error trying to run psi quantification `ERROR: LoadError: BoundsError: attempt to access 35nt DNA Sequence: CGGGTGCTTTCTGCCCACCCCCTGCTCTTGCCAGC at index [31:36] Stacktrace: [1] checkbounds(::BioSequences.BioSequence{BioSequences.DNAAlphabet{2}}, ::UnitRange{Int64}) at /home/jordi/.julia/v0.6/BioSequences/src/bioseq/indexing.jl:15 [2] BioSequences.BioSequence(::BioSequences.BioSequence{BioSequences.DNAAlphabet{2}}, ::UnitRange{Int64}) at /home/jordi/.julia/v0.6/BioSequences/src/bioseq/constructors.jl:33...

jordi-vaquero

ArgumentError with whippet-delta.jl

2

Hi Tim @timbitz I have used Whippet successfully on a few different files and cell types. In my current experiment I have several comparisons to make, each one with the...

mmilevskiy

Addition of Dockerfile for version 0.11

1

Addition of Dockerfile for version 0.11 Locally it works for me. The commands are called without the bin prefix as shown below: `julia whippet-index.jl --help` and not `julia bin/whippet-index.jl --help`...

fgypas

Dockerfile for Whippet.jl

2

Hi Do you have any Dockefile available for whippet? Thank you in advance Foivos

fgypas