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Hey Alex,
I'd appreciate it if you could clarify how/when antisense-orientation reads are counted in the CellReads.stats table. I noticed that no matter what settings I've used (i.e. Gene, GeneFul…
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I have some bulk RNA-Seq data that I want to also count reads in introns as well as exons. Is the `-soloFeatures GeneFull` option only available in STARsolo or can the regular STAR do it as well?
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Hello,
My understanding is that the `coord` column contains the coordinates of the _splicing event_ (e.g. the coordinates may be that of a skipped exon) and not the genomic coordinates of the seque…
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Hello. I installed gffread 0.12.1 through anaconda and used to convert a GFF3 file into GTF format.
The file I used is the gff3 annotation file from Araport11:
[https://www.arabidopsis.org/download_…
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Hi,
I am experiencing an issue with 3 of my 5 BAM files where the **USED** value is 0, and the majority of reads are classified as **NOT_NH_1**, which is associated with multimapped reads. However, t…
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I was looking at the gene annotation files, in particular, http://courtyard.gi.ucsc.edu/~mhauknes/T2T/t2t_Y/annotation_set/CHM13.v2.0.gff3
It looks like the file contains multiple problems, mostly to…
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Hello everyone,
I have been using ASGAL for some time now and I'm very content with the obtained results, congrats on the implementation.
Lately I have been working with samples that present the [AL…
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Where can I find more information on how to create the panel and the sample fies?
I went through the [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6752313/pdf/41436_2019_Article_475.pdf) an…
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Hello, thank for this tool. I would like to report what I think is a bug. Honestly, I am not sure if I am using in right way the tool or maybe is in fact a bug.
I work with Nanopore data to ident…
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Hello,
the gene in question is ENSG00000006062.
I can retrieve its full sequence fine, but I cannot retrieve upstream of it (for whatever reason).
The error I get from the website is (https://…