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Greetings,
I am working with data obtained from shRNA screens performed using Affymetrix arrays. I am trying to prepare the file containing LogFC between T2 and T0; however, I have cases in which t…
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Hello,
I have a two-part question regarding the newer Mixscape tool as it relates to the downstream results based on whether or not perturbation targets are considered variable for analysis. I am a…
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Hi,
When I use the nanopolish 0.13.2 to detect the polyA tail, I get saome issues. I can finish nanopolish index. Then, I run 'nanopolish polya'. The errors are as follows:
How can I fix i…
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I downloaded the [rat rn6 genome](http://crispor.tefor.net/genomes/rn6/) provided on the CRISPOR website, and tried to use it to find off-target locations for gRNAs using a .bed file as an input. This…
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at the end of the notebook, the results of the work are stored in files that use the template:
`"{}_gRNA_targets".format(target_gene_id)`
Please use the EuPaGDT job name instead of target_gene_id
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Is there a way to manually create the subsequence that will be searched by the EuPaGDT server? After having inserted by gRNA into the sequence I want to be able to use THAT sequence in this tool to t…
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Hi @ drivenbyentropy,
Thanks for the great port of the RNA fold tool! My initial tests have worked out really well, and I'd like to incorporate as a scoring metric into our CRISPR guide selection t…
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When I'm looking at the results in the notebook, it would be very helpful to be able to distinguish the gRNA sequence from the PAM suffix in the results. Please make:
- the last 3 letters of the s…
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Hi,
I have ScRNA and ScATAC data from same experiment (not multiomic) and I followed the merge vignette to merge the 5 samples (2 groups) based on intersecting peaks as shown in the vignette.
Comin…
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The `append` method should merge RDF graphs and update SBOL Documents accordingly. Currently, some data and objects in the SBOL Document tree are being duplicated when merging. This is strange, beca…