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Hello,
I am simulating reads in transcriptome mode. For this purpose, I have created an expression profile in the specified format. The read counts generated per transcript are different from what…
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## Check Documentation
I have checked the following places for your error:
I have checked both of these and looked through the introduction to see which steps might require the genome.
- [x] …
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just like the title。
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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, …
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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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When I run my own data for alignment with Star, I encountered a bug. I am debugging now to see what happens. I noticed that Salmon as the quantifier tool, is not affected at all. It …
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The Flux simulator seems to not respect the _effective length_ of transcripts during it's simulation. This means that quantification tools that "correctly" adjust for effective length will be penaliz…
rob-p updated
8 years ago
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Hello,
I'm trying to use STARsolo to count genes and SJ from 10X 3' scRNA data and then I want to use RSEM for isoform quantification. Currently, I'm using STAR v2.7.10b.
First, I generated a re…
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Hello, team.
First I want to say thanks to this nice tool.
Other functions in this tool work good like _genotype_. in my single cell RNA sequencing data (+single end).
I downloaded this tool f…
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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…