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Drop-seq

Introduction

Drop-seq are java tools for analyzing Drop-seq data.

For more information, please check:

Versions

  • 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

Module

You can load the modules by:

module load biocontainers
module load drop-seq

Example 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