Bioinformatics

Adding +1 to exon end.

1

From a gtf where coordinate is chr3 52554724 52554879 for an exon. Looking into _genes.ent output then for this same exon : chr3 52554724 52554880 It's always adding 1 to...

data conversion from different Hi-C contact matrices bin size

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> bash ./hic2give ./ test.hic giveInteraction.bed 40000 > bin size that user wants to extract the data from (please make sure the bin size you entered is contained in the...

I have deployed GIVE with GIVE-Docker. From the ChIA-PET Long Range Interaction example running, I started to remove and add new stuffs in this docker container. But the panel on...

Is is possible to load reference annotation as gtf or gff from gencode/ensembl?

1

Is add_geneAnnot.sh only working with UCSC annotation ?

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]...

It could be cool to have this option to draw lines over the heatmap to separate some region manually. Something like here , [example with one vertical line](https://github.com/jokergoo/EnrichedHeatmap)