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First, thank you so much for this wonderful tool! I'm encountering issues with certain timepoints of a stranded RNA-seq experiment where they do not pass IRFinder's directionality test. I am guessing …
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Dear authors,
I want to calculate the spliced/unspliced gene ratio but I am not sure what to do with the ambiguous count table. Should I just remove it or combine it to one of the spliced or unspli…
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Dear Dr Qiu,
Thank you very much for this great package. I found you use tow data sets in scNT-seq. One is splicing dataset. Another is labeling dataset. Splicing dataset can get the spliced and un…
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Hi there,
Thank you so much for this amazing tool!
I am just wondering if it is possible to get a more in-depth explanation of each parameter for the config file e.g. for isoform parameters?
…
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At the moment, for each norminal pvalue, we have the following information:
`molecular_trait_object_id `
`molecular_trait_id `(ID of the molecular trait used for QTL mapping. Depending on the quan…
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Hello,
I am working with data that has spike-ins and processing it in USA mode. I noticed that after generating the transcript-to-gene file by means of the provided code from the tutorial 'Resolvi…
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Hello,
I am testing alevin-fry on some public sc-RNAseq data (GEO accession: GSE81076). The issue that I have is that when I process the gene count x cell matrix in R and perform per-cell metrics,…
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**Hi,
I'm opening this thread to ask you about the error from GDCdownload() function to download splice junction data.
My codes are as follows:**
#Download splicing variants data
stad.junct…
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Dear EduEyras
I analyzed my own RNA-seq data with SUPPA2，and encountered some question.
when I use the test data you provided, the SUPPA2 is running without any error. but when I used SUPPA2 to ana…
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Hello again.
I originally posted about a "Difference in Agrp expression depending on alignment strategy" (https://github.com/COMBINE-lab/alevin-fry/issues/81)
I closed the issue, since the issue…