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Hi,
I am trying to analyze RNA Modifications in Direct RNA-seq nanopore datasets. I performed the sequencing using rat cell line, so my reference is Rnor_6. I am trying to perform resquiggle on my F…
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In the current code to merge SCE objects, we subset all SCEs (the RNA experiments, specifically) to only include the intersection of genes in the final merged object. We may want to expand this to ins…
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@bsamad observes (and I have observed in the past) that if you run the following manifest:
```
@table = table(
[ 'rna_seq',
[ 'compartment', '::equals', 'tumor' ],
[ 'sample', 'patient…
graft updated
4 years ago
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# Issue Report
## Please describe the issue:
While conducting basecalling on direct RNA samples, I've noticed a discrepancy between the number of base-called bases and the estimated length of po…
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I'd like to use the `integrate_ChIP_RNA()` function to find the targets of my TF of interest. I have the RNA-seq differential gene expression result (TF inhibitor drug vs. vehicle control RNA-seq data…
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Hello. I was reviewing some of my recent RNA004 direct RNA seq data to see what modifications I could call from them. I have six replicates here, and I called m6A, m5C, and pseudouridine for all of th…
mbosm updated
3 weeks ago
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Hello, I have encounter a new issue when running the scRNA-sequencing. And the error message is below. At first I thought it was due to the pandas package so I updated my pandas to the latest version…
yc508 updated
10 months ago
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Hi,
I tried to run poreplex on a minION run using the follwing command to basecall and demultiplex barcodes from direct RNA sequencing:
` poreplex -i 20191122_1000_MN24929_FAL01495_e9928ec8/fast5/ -…
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I am running locally and installed via the installation command at http://rail.bio. I ran with the following command:
rail-rna go local -x /path/Homo_sapiens/UCSC/hg38/Sequence/BowtieIndex/geno…
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Hi,
Harold and I were talking today and ended looking at this term. There are both some minor issues and some major issues (which I've put in SF before). At a minimum, we should fix the minor issues.…