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# Change old content
- [ ] back up and deprecate old Apollo2
- [ ] back up and deprecate old fasta files in BLAST
- [ ] back up and deprecate old fasta files in Hmmer
# Add new content to i5k …
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# OGS remapping and manual annotations
- [ ] request whole-genome alignment
- [ ] Set up data directories and get data
- [ ] run remap-gff3
# Change old content
- [ ] back up and deprecate ol…
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Let's try to use regtools for this.
- regtools junctions-extract function: https://regtools.readthedocs.io/en/latest/commands/junctions-extract/
- parameters to specify:
- `-m 20` (should matc…
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# Update May 28th
Today, I was able to complete the pipeline up till deseq2 or possibly featurecounts. The Star script is finished, and now, within the Star rule, I am using samtools to separate th…
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read_json almost never work for me. Here is for instance a json that is totally valid but breaks read_json
```
{
"id" : "GSM1698568",
"gse" : [
"GSE69360"
],
"title" : "Biochain_Adu…
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I have tried running both the run_ORQAS.sh script and running the pipeline step by step. I have tried using my ownrnaseq and riboseq data and the sample data. I keep getting the same error.
termin…
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It's currently not possible to import an experiment where there are multiple bioassays for the same biomaterial.
The simplest example of this scenario is a dataset with technical replicates where a g…
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Create a data migration process that migrates Experiment-specific data to Amazon S3 buckets. The program triggers a data transfer between the local file system and our S3 buckets.
Only data associat…
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Hello,
I'm getting an error when trying to run croo after a successful run of the encode rna-seq-pipeline. My version of croo is 0.6.0
The command I ran is
`croo /storage/aadams/scripts/encode…