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Hello,
I would like to run factR2 on a custom assembly where I ran in the issue described in [https://github.com/f-hamidlab/factR2/issues/7](issue#7). So I thought I try it on the example data you …
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What is the motivation for assembling the Transcriptome with trinity and translating that, rather than mapping the Transcriptome data to the assembly and building gene models that way?
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Currently working on a manuscript for which this term would be perfect. It exists in The Software Ontology (link in OLS below). Perhaps the format should be transcriptome assembly assay?
NTR: tran…
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Hello,
I found a few contradicting posts in bioinformatics forums whether Megahit could be used or must not be used for metatranscriptome assemblies from microbiome meta-RNA-seq data. I have it a …
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The Megakaryocyte_rep2 data is much smaller than the other samples. Is this intended? In https://www.ncbi.nlm.nih.gov/sra/?term=SRR549358 the original data of the two samples is about the same size. I…
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Right now, assembly groups are a user-input parameter.
## Background
- Deciding which samples should be assembled together is difficult. Co-assembly of multiple samples can improve recovery of ass…
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I'm reaching out regarding an issue I encountered while using RNA-bloom version 2.0.1 in conjunction with JDK17. Specifically, I'm attempting to generate a de novo assembly using 32 samples of transcr…
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Hello Again,
I'm attempting to run EGAP on a new assembled genome and am getting a new error. Attached will be the code submitted via shell script and a portion of the slurm file output. This new g…
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OGS v1.2 is here: https://i5k.nal.usda.gov/bio_data/836678
The community wants to review these assemblies, and having the OGS on each haplotype will likely help. The OGS will need to be remapped fi…
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These organism either do not have a link to Jbrowse or need Jbrowse done for them.
- [x] Acer saccharum - Transcriptome Assembly
- [x] Alnus rhombifolia - Transcriptome Assembly
- [x] Alnus rubra…