Software: Drop-seq
Description
Drop-seq are java tools for analyzing Drop-seq data.
Available Versions
| Unspecified: | 2.5.2 |
|---|
Home page: https://github.com/broadinstitute/Drop-seq
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
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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