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Hi team,
Thanks for a great resource. I've been struggling for a few days to troubleshoot this issue. I'm getting a very cryptic index error when trying to run the redesign Chain A in this notebook…
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Hello, I am trying to run the Stacks2 pipeline on single end data. I had no issues until I reached tvs2bam where I got an error. This error seems to be caused by the "Short read data from individuals"…
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Dear nanopore devs,
I'm having issues getting mini_assemble to run on human (HG001/NA12978) data. I've successfully ran it on smaller assemblies before, but a ~30x human genome seems to be causing …
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Hi there,
Can I use trgt to call repeat expansions from short read data (illlumina data for example) ? If yes, is there any caveat?
Thanks in advance.
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When using `cosmic_fit` to assign mutational signatures to my samples, I identified SBS1, SBS5, and SBS19.
I then extracted these three signatures to refit using `denovo_fit`. However, I noticed di…
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Hi. Thank you for your nice tool!
I have a poorly annotated transcriptome file in my species Aiptasia. This file lacks isoform level annotation and all the isoforms are removed. I am wondering is…
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Hi Heng,
Great tool. Do you have any advice for joint calling of multiple samples?
I obtained a reasonable looking call set by first running your `run-calling` script on each sample individually. …
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The setup:
Basic MNIST model as proof of concept using pytorch lightning with xla libraries on top of the Neuron DLAMI. Training on 2 Neuron cores (trn1.2xlarge) works well and successfully calls t…
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usearch is frequently used for chimera checking, but due to the RAM limitation, only small data sets can be assessed, or else the data needs to be broken up into subsearches (my current approach). vs…