<commit_before># Template for scRNA-seq using Illumina prepared samples
#
# Drosophila melanogaster
# 2018-03-16
#
# FlyBase
# Genome build: BDGP6
# Release version: 6.19
# FASTA: ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/fasta/
# Concatenate these FASTA files:
# - dmel-all-miRNA-r6.19.fasta.gz
# - dmel-all-miscRNA-r6.19.fasta.gz
# - dmel-all-ncRNA-r6.19.fasta.gz
# - dmel-all-pseudogene-r6.19.fasta.gz
# - dmel-all-tRNA-r6.19.fasta.gz
# GTF: ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gtf/dmel-all-r6.19.gtf.gz
#
# NOTE: genome_build is specific to bcbio install
---
details:
  - analysis: scRNA-seq
    genome_build: BDGP6_6.19
    algorithm:
      cellular_barcode_correction: 1
      minimum_barcode_depth: 1000
      sample_barcodes: sample_barcodes_reverse_complement.txt
      # singlecell_quantifier: rapmap
      transcriptome_fasta: dmel-all-concatenated-r6.19.fasta
      transcriptome_gtf: dmel-all-r6.19.gtf
      umi_type: harvard-indrop-v3
upload:
  dir: ../final
<commit_msg>Update dmelanogaster.yaml<commit_after># Template for scRNA-seq using Illumina prepared samples
#
# Drosophila melanogaster
# 2018-04-30
#
# FlyBase
# Genome build: BDGP6
# Release version: 6.19
# FASTA: ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/fasta/
# Concatenate these FASTA files:
# - dmel-all-miRNA-r6.19.fasta.gz
# - dmel-all-miscRNA-r6.19.fasta.gz
# - dmel-all-ncRNA-r6.19.fasta.gz
# - dmel-all-pseudogene-r6.19.fasta.gz
# - dmel-all-tRNA-r6.19.fasta.gz
# GTF: ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gtf/dmel-all-r6.19.gtf.gz
#
# NOTE: genome_build is specific to bcbio install
---
details:
  - analysis: scRNA-seq
    genome_build: BDGP6_6.19
    algorithm:
      cellular_barcode_correction: 1
      minimum_barcode_depth: 1000
      sample_barcodes: sample_barcodes_reverse_complement.txt
      # singlecell_quantifier: rapmap
      transcriptome_fasta: dmel-all-concatenated-r6.19.fasta
      transcriptome_gtf: dmel-all-r6.19.gtf
      umi_type: harvard-indrop-v3
upload:
  dir: ../final

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