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Hello,
I tried creating a salmon index for bos taurus but was not successful. I created the decoy file using:
grep "^>" decoys.txt
sed -i.bak -e 's/>//g' decoys.txt
When i try to index usin…
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Hello, I have basic questions about most of scripts in this website
https://github.com/trinityrnaseq/RagonInst_Sept2017_Workshop/wiki/assembly_quality_assessment
excuse me for not having background…
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Hi, if I have multiple sets of transcriptome data can I input it at the same time?
for example:
./fungap.py --genome_assembly /data/zhaochi/w5.contigs.fasta --trans_read_1 /data/zhaochi/T1_1.fastq /…
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**Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?**
The bug is related to building the index by combining genome and transcriptome reference.
**Describe the bug**
…
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Hi,
I started to use RSEM, and I am happy with what it can do!
I would like to use it further, to be able to pick the most abundant isoform of each gene, therefore wanted to try `rsem-calculate-ex…
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Hello
We are currently trying to use Salmon quant mode with BAM files that were generated from another lab's work. We have continued to get the error below and are unsure what the problem is. Our or…
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Hi there,
I have been trying to use the Stringtie-ballgown pipeline to conduct a differential expression analysis of the isoforms.
So here is the overview procedures I have taken:
1. Strin…
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[A8_results_out.log](https://github.com/mrmckain/Fast-Plast/files/5752719/A8_results_out.log)
[A8_Fast-Plast_Progress.log](https://github.com/mrmckain/Fast-Plast/files/5752720/A8_Fast-Plast_Progres…
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The assembly prefix should be consistent with transxpress-nextflow, which is currently:
```
MMDD_GENUS_SPECIES_ASSEMBLER
```
e.g.
```
0222_Chattonella_subsalsa_Trinity
```
Additionally, the…
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see https://github.com/dib-lab/eelpond/issues/103#issuecomment-471185817 for initial motivation --
I think we need a modular way to do high-level correctness checking.
e.g.,
* if `quantify`…