# Template for scRNA-seq using Illumina prepared samples
#
# Drosophila melanogaster
# 2018-04-30
#
# FlyBase
# FASTA: seqcloud fasta dmelanogaster cdna
# GTF: seqcloud gtf dmelanogaster
#
# NOTE: genome_build is specific to bcbio install
---
details:
  - analysis: scRNA-seq
    genome_build: BDGP6_FlyBase
    algorithm:
      cellular_barcode_correction: 1
      minimum_barcode_depth: 1000
      sample_barcodes: sample_barcodes_reverse_complement.txt
      # singlecell_quantifier: rapmap
      transcriptome_fasta: dmel-all-concatenated-${FLYBASE_RELEASE_VERSION}.fasta
      transcriptome_gtf: dmel-all-${FLYBASE_RELEASE_VERSION}.gtf
      umi_type: harvard-indrop-v3
upload:
  dir: ../final

# Template for scRNA-seq using Illumina prepared samples
#
# Drosophila melanogaster
# 2018-04-30
#
# FlyBase
# FASTA: seqcloud fasta dmelanogaster cdna
# GTF: seqcloud gtf dmelanogaster
#
# NOTE: genome_build is specific to bcbio install
---
details:
  - analysis: scRNA-seq
    genome_build: BDGP6_FlyBase
    algorithm:
      cellular_barcode_correction: 1
      minimum_barcode_depth: 1000
      sample_barcodes: sample_barcodes_reverse_complement.txt
      # singlecell_quantifier: rapmap
      transcriptome_fasta: dmel-transcriptome-r6.21.fasta
      transcriptome_gtf: dmel-all-r6.21.gtf
      umi_type: harvard-indrop-v3
upload:
  dir: ../final

Update FASTA and GTF scripts
Update FASTA and GTF scripts
