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Hi,
I am hoping to perform transcriptome assembly using both nanopore long read sequencing data and illumina short read sequencing data. It appears RATTLE only permits the use of long read sequenci…
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Hi, I am trying to run the sequences section of Trinotate but run into an error with the tmhmmv2 command:
```
[Wed Sep 11 15:47:29 2024] Running CMD: tmhmm --short /data/putnamlab/dbecks/Heatwave_…
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Hello,
and thank you for this amazing tool. I am currently examining different methods of hybrid de novo transcriptome assembly.
I constructed various assemblies from mouse data and compared their…
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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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I want to open a discussion about **which information one should provide in the pull request**.
- Maybe having a copyable template with bullet-points addressing the annotation process would be help…
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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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Hi authors, great paper just a couple of nitpicks in the paper that might make it a little clearer.
1.
To use it you have to provide a set of contigs resulting of a de novo transcriptome assembly…