Scripts for running different algorithms using Slurm in the Cluster.
- ScriptExample.sbs -> classical parameters to slurm scripts.
- script_bwa.sbs -> exomes alignment with BWA mem (iterative).
- script_fastqc -> QC of fastq (iterative).
- Slurm_Rscripts -> structure for a Rscript in slurm.
- SingeCell_CellRanger_Mkfastq.sbs -> 10X demultiplexing script.
- SingeCell_CellRanger_Counts.sbs -> 10X alignment (STAR) and secondary analysis.
- script_bcl2fastq.sbs -> custom demultiplexing (Illumina based).
- script_quant3p.sbs -> RNAseq cuantification.
- script_variantCalling.sbs -> variant calling with Seurat (not working yet), MuTect2, Strelka and VarScan2 (iterative).
- tables_rawdata.sbs -> make a table with basic information: number of bases, number of reads, % of GC, quality...
Install_RPackages_Cluster.R -> how to install packages in a specific user folder (and add it to .Rprofile).