Whippet.jl
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timbitz
Lightweight and Fast; RNA-seq quantification at the event-level
Hi there, I am trying to use Whippet in Julia and have managed to get all dependencies installed. However, I got the following error during installation and when testing Whippet:...
Hello all, I would like to know if whippet is adapted for long reads and if anyone has already used it on Nanopore long read RNA-seq Thank you for your...
Hello, I generated the Whippet index file: ``` julia bin/whippet-index.jl --fasta data/genomes/fasta/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz --gtf data/transcriptomes/gencode/gencode.v34/gencode.v34.annotation.gtf.gz --index data/whippet_index ``` And then approached to run the quantification: ``` julia /home/bd1/tools/Whippet.jl/bin/whippet-quant.jl /home/bd1/mds-datasets-no-backup/dataset2/fastq/SRR6781235_1.fastq.gz /home/bd1/mds-datasets-no-backup/dataset2/fastq/SRR6781235_2.fastq.gz -x...
Hello Sir, I was trying to run the first command i.e. julia bin/whippet-index.jl --fasta hg19.fa.gz --gtf anno/gencode_hg19.v25.tsl1.gtf.gz, but it is showing the following error constantly.It would be nice have your...
Dear Tim, I have come across an issue when running `julia --project -e 'using Pkg; Pkg.instantiate(); Pkg.test()'` as below I guess there is something wrong with the dependant package "WaveletMtrices"....
Hi, I am getting some error when running Whippet-index.jl, where it complains that it is out of bounds, even though it should still be within the the reference genome: ```...
Hello, I installed [julia](https://julialang.org/downloads/) for Red Hat 8.4 Linux. When I tried running Whippet, e.g. `whippet-index.jl --fasta /reference/homo_sapiens/GRCh38/ensembl/release-96/Sequence/WholeGenomeFasta/Homo_sapiens.GRCh38.dna.primary_assembly.fa --gtf /export/apps/opt/Whippet/1.6.1/anno/refseq_hg19.flat.gz` I got multiple errors complaining about missing Julia packages. In...
