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Hello,
I have some CAGE sequencing data from oil palm. The reads were mapped to the genome. I have alignment BAM file, and converted into BigWig. I have problem running quantifyCTSSs because I couldn…
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Hello,
Thanks for developing the tool. Does this tool work with non-model species of different ploidy?
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Hi:
I am studying a non-model diploid mammal species with a large genome size (~6GB). I have 30X Hifi data, as well as Hi-C data from Dovetail Genomics using their Chicago libraries. I have made an a…
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Hi:
I am studying a non-model diploid mammal species with a large genome size (~6GB). I have 30X Hifi data, as well as Hi-C data from Dovetail Genomics using their Chicago libraries. I have made an a…
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Hi,
I'm quite excited to use SQuIRE, but I work on a non-UCSC genome, with no files to "fetch". Would it be possible to make available the formats of the "fetch" files, but also potentially an opti…
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Hello,
Wondering if it's possible to build indexes for quick genotyping of low coverage samples ( ~2-5x ~1500+) from a set of samples generated at higher coverage (~500, 10-20x) for a fish species …
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Hi,
I would like to use casper to find CN from bulk RNA-seq data of mouse and chicken.
I have followed successfully the instruction until the function "generateAnnotation".
However since thi…
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Hello Tomas,
On the corner plot of `plot_posterior()`, it might be practical to show with points the parameter values of the models that were available during the fit to help evaluate easily, visua…
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Can we have a metric on the website about the number of genes in GO-CAM models (by species)
i.e. a non-redundant list of genes that are causally connected (obviously, some genes will be in mul…
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Hi,
I am trying to perform GO enrichment analysis for non-model plants. Please let me know if I can use GO_MWU with non-model species for GO enrichment analysis.
I tried to download a gaf file (a…