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Hi, I am confused of the pathogenicity annotation of splice_site mutation.
In two articles recently published in NEJM, one classified splice variants affecting penultimate and the last exon as VUS or…
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Enjoying the great tool, but I have another question:
One of my sample had following stats of used and unused reads (following the 2-pass alignment strategy with STAR)
read outcome totals across a…
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Hi salmon team,
Thank you for developing this useful tool! I used salmon (v1.9.0) to quantify transcript abundance using full-length cDNA reads (ONT) after mapping with minimap2 to a transcriptome …
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Hello there,
I was getting Psi scores of 0.5 for events that are definitely 100% included and Psi should be 1. Any idea why this might be happening?
Here's the event:
![image](https://f.cloud.github.…
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Hi, how to deal with multiple variants in a small region, is there a way to combine them to one variant by Pisces or other tools? Attached file describes the situation we find about EGFR exon 19 delet…
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Hi,
I have a stringtie output in gff3, but parsing with gff3_validator, it provides me the following output:
Fatal Error: cannot parse ID from entry
Scaffold_2 StringTie exon 38612 …
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Hello,
I am getting an empty CDS file from running gff2seq with no error message.
My command is `anchorwave gff2seq -i GCF_003119195.2_ASM311919v2_genomic.gff -r GCF_003119195.2_ASM311919v2_genom…
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Hi,
I am interested in aligning my long read data using your pipeline in hopes of getting better alignment of the reads. I ran your example and runs fine for me but when I run my data, it errors. …
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I'm trying to run mfannot on a number of yeast mitochondrial assemblies. Nearly all of them worked perfectly but I am getting two separate errors in two separate assemblies. The command to run all of …
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When I run this command, it will report an error indicating that the tag transcript_id cannot be found in a certain line.
vg autoindex --threads 5 --gff-feature exon --gff-tx-tag transcript_id --wo…