Workflows

MMGBSA simulation and calculation

Run baredSC in 1 dimension in logNorm for 1 to N gaussians and combine models.

Automated inference of stable isotope incorporation rates in proteins for functional metaproteomics

We assume the identifiers of the input list are like: sample_name_replicateID. The identifiers of the output list will be: sample_name

Racon polish with long reads, x4

Downloads fastq files for sequencing run accessions provided in a text file using fasterq-dump. Creates one job per listed run accession.

This workflow takes as input SR BAM from ChIP-seq. It calls peaks on each replicate and intersect them. In parallel, each BAM is subsetted to smallest number of reads. Peaks are called using both subsets combined. Only peaks called using a combination of both subsets which have summits intersecting the intersection of both replicates will be kept.

Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring

This workflow take as input a collection of paired fastq. Remove adapters with cutadapt, map pairs with bowtie2 allowing dovetail. Keep MAPQ30 and concordant pairs. BAM to BED. MACS2 with "ATAC" parameters.

This workflow take as input a collection of paired fastq. It uses HiCUP to go from fastq to validPair file. The pairs are filtered for MAPQ and sorted by cooler to generate a tabix dataset. Cooler is used to generate a balanced cool file to the desired resolution.