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This step is missing from the Transdecoder predictions. I think it is helpful & should be implemented, as it seems to improve the N-terminal prediction (trains an HMM that does it; perhaps it picks u…
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My nextflow runs on LSF cluster occasionally fail with this error message:
```
ERROR ~ Error executing process > 'kallisto'
Caused by:
Missing output file(s) `kallisto.isoform.TPM.not_cross_nor…
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When I try to run the annotation pipeline I keep getting this error. I think it has to do with calling a user-database. I have a fasta file that I want to use for annotation.
Here is the dammit log…
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ghost updated
5 years ago
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ghost updated
5 years ago
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@colleenburge and I are working with a subset of eelgrass transcriptomics data from Trinity. [This file](https://github.com/eimd-2019/project-EWD-transcriptomics/blob/master/data/2019-07-09-Merging-Sc…
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ghost updated
5 years ago
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If using PASA output transcripts as input into TransDecoder is it appropriate to use the '-S' flag? I guessed yes but now I am wondering if that was correct.
Thanks,
John Martinson
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Hi,
we're working on a eukaryotic genome (fish) with no reference genome. It has a near relative with an annotated transcriptome. I have mapped my fastq file to the near relative and got ~80% mapping…
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(update this appears to be purely a paths problem. running this file (https://github.com/transXpress/transXpress-snakemake/blob/f83f73c246d3fa0f94552c58bfbb52f1c449aeb2/run_tak.sh) fixed it
On 56d0…