Drop-seq

Introduction

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

For more information, please check:
Home page: https://github.com/broadinstitute/Drop-seq

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