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Dear developers,
I'm trying to identify a fusion break that seems to occur in introns with a very very low expression value. I have only 7 read pairs out of 15 million read pairs for the fusion gene.…
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Here are some DFE inference papers to get the BGS modeling conversation started. Please feel free to add any that I have missed!
Keightley & Eyre Walker 2007 (humans and drosophila) https://www.gen…
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Improve various aspects of parental gene assignment for transcripts creates from long-read data
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Hi,
I am trying to use BRIE using a custom annotation file and the GENCODE M10 annotation file. In both cases, running `brie-event` as follows:
`brie-event -a gencode.vM10.annotation.gtf`
ret…
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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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As it turn out. The gene.gtf file provided in out snuc study is exon based instead of gene based. This create a lot of records with duplicates gene IDs but different start-end position and may leads t…
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[Annotations.gff3.gz](https://github.com/GMOD/Apollo/files/3065740/Annotations.gff3.gz)
[Cam_Hsc_genes_v1_UTRs-Hsc_scaff001-1..6046013.gff3.gz](https://github.com/GMOD/Apollo/files/3065749/Cam_Hsc_…
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Hello,
I have been unable to complete my ExOrthist run because of the following error:
ERROR : Unknown image format/type: /nfs/users/lserrano/lciampi/JuanRamon/Orthologies/ExOrthist/singularity…
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Hi, I am analyzing a dataset with several samples that I plan to use for downstream analysis of both gene level and transcript level analyses. I noticed an issue with the gene count matrix generated…
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Dir Sir, I tried to run DCC, but I failed every time at step 'Filter by non repetitive region'.
Could you help me to fix it?
Here is the command:
/data/suyao/tools/build/bin/DCC @/data/suyao/proje…