rnaseq-pipeline
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PavlidisLab
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
``` srun: error: unable to initialize step context socket: Address already in use srun: error: Unable to create step for job 2539557: Address already in use ```
Tasks that should be covered via sub-commands: - submit experiments from a gsheet - submit experiments from a file - submit individual experiment - resubmit batch information - general luigi-wrapper...
I think there's a delay between batch info submission and the batch factor appearing in the Gemma public API due to caching. A simple workaround would be to introduce a...
We don't use split spots (required for --skip-technical) and we trim adapter ourselves, so there's no need for these two options.
This will have the advantage of grouping the alignments statistics with the FASTQ quality controls in the final report.
Caught this error while aligning GSM7062734 from GSE226076.
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RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.