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Hello,
I just tried out starchip. I have no problem with step 1
```
$ ./Step1.sh
Filtering out chimeric reads that appear circular
Filtering circular reads based on assigned thresholds of 5 r…
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Hi,
thanks for developing this cool tool!
I'm trying to use mm10 (obtained using fetch ) to quantify some RNA-seq libraries, then I noticed a weird warning at the **Count** procedure :
`Warning: …
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Hello, everyone.
The **Introduction to RNA-seq** is currently empty, so I would like to contribute to it.
As far as I understood it, this episode should contain instructions on how to go from r…
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Great tool that integrates lots of functions!
I was wondering if there is a way to get the isoform counts. I was trying to get the isoform counts following your Nature paper (specifically https://g…
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Hi!
I'm working with crb-blast for the first time and was able to use it without any obvious trouble (exit status 0) - running a query squid transcriptome against target single genomes for 10 speci…
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Some tool choices in RNAseq are a matter preference, in that the evidence is not clear enough to enable an empirically or theoretically motivated choice. However, some things are just demonstrably bad…
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Hi ALex
I have retrieved the fasta sequences from a bed file using the bedtools (without specifying the strand information), and then I treated each sequence as a gene and combined it with a human r…
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Hi,
Thanks for the great tool.
As the title, I'm wondering if this tool can be applied to simulate single cell Nanopore reads. I'm thinking to generate bunch of transcripts for a gene and attach th…
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Sample-specific sorted BAM files can be found in each sample-specific subdirectory here:
https://gannet.fish.washington.edu/Atumefaciens/20210726_cvir_stringtie_GCF_002022765.2_isoforms/
There's…
kubu4 updated
2 years ago
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Instead of indexing the transcriptome at the start of each code block, I have indexed a copy of mm10 on AFW. Can this be changed in the code?
i.e.
rule quant_salmon:
input:
R1 = con…