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I'm trying to use featureCounts to quantify lncRNA data, the lncRNA gtf file is generated from stringtie. I find that the expression matrix is different from the matrix generated by stringtie.Which so…
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Hi
I'm trying to replicate some splice junctions in my long-read Kinnex data. Out of a total of 115 splice junctions, I managed to replicate about 100 from quantification obtained via the isoseq/SQ…
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PAQR performs quantification of PAS usage based on the weighted average exon length.
It is rather straightforward to test for differential PAS usage as the conditions are anyway supplied in the samp…
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Hi,
We (@zzare-umd, @NPSDC, and I) are trying to do some analysis of different transcript identification and quantification tools using the benchmarking data you're providing through this project…
rob-p updated
5 months ago
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Hi,
I am trying the tool for the quantification of nuclear RNA, after my recent tweets with Lior Patcher.
Every commands in the Velocity tutorial seems to work, but I want only the quantificatio…
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For gene-body internal last exons currently the uniquely-exonic regions for each last exon are passed as regions for Salmon to quantify. e.g. for a bleedthrough event, the annotated internal exon is s…
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Hi,
When I download legacy exon quantification from *TCGAbiolinks*, the resulting `SummarizedExperiment` I get has the `@rowRanges` contain `start`, `end`, and `chromosome`.
It would be great if…
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Hello!
I'm working on large cohort with thousands of samples ( > 100 TB). However, due to the limitation of storage, it is not possible to keep all aligned reads at the same time. I found no matte…
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Hi Geo,
I have nanopore cDNA data aligned with minimap2 (with --cs --MD). I tried abundance estimation with StringTie v1.3.5 that should recognize the "CS" tag as an alternative to "XS". The splice…
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Dear T2T-CHM13 team,
I have been scanning through the UCSC Gencode v35 gff3 annotation file and found that the gene EPHA2 lacked a parent gene entry. The annotation file contains transcript, exon, …