Introduction ~~~~~~~~ Drop-seq are java tools for analyzing Drop-seq data.
Home page: https://github.com/broadinstitute/Drop-seq
- 2.5.2
Commands ~~~~~~~ - AssignCellsToSamples - BamTagHistogram - BamTagOfTagCounts - BaseDistributionAtReadPosition - BipartiteRabiesVirusCollapse - CensusSeq - CollapseBarcodesInPlace - CollapseTagWithContext - CompareDropSeqAlignments - ComputeUMISharing - ConvertTagToReadGroup - ConvertToRefFlat - CountUnmatchedSampleIndices - CreateIntervalsFiles - CreateMetaCells - CreateSnpIntervalFromVcf - CsiAnalysis - DetectBeadSubstitutionErrors - DetectBeadSynthesisErrors - DetectDoublets - DigitalExpression - DownsampleBamByTag - DownsampleTranscriptsAndQuantiles - Drop-seq_Alignment_Cookbook.pdf - Drop-seq_alignment.sh - FilterBam - FilterBamByGeneFunction - FilterBamByTag - FilterDge - FilterGtf - FilterValidRabiesBarcodes - GatherGeneGCLength - GatherMolecularBarcodeDistributionByGene - GatherReadQualityMetrics - GenotypeSperm - MaskReferenceSequence - MergeDgeSparse - PolyATrimmer - ReduceGtf - RollCall - SelectCellsByNumTranscripts - SignTest - SingleCellRnaSeqMetricsCollector - SpermSeqMarkDuplicates - SplitBamByCell - TagBam - TagBamWithReadSequenceExtended - TagReadWithGeneExonFunction - TagReadWithGeneFunction - TagReadWithInterval - TagReadWithRabiesBarcodes - TrimStartingSequence - ValidateAlignedSam - ValidateReference - create_Drop-seq_reference_metadata.sh
You can load the modules by:
module load biocontainers
module load drop-seqExample job ~~~~~ .. warning:: Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run drop-seq on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=drop-seq
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers drop-seq