/umic

barcode counting for inDrops3 single cell RNA-seq protocol

Primary LanguageC++MIT LicenseMIT

summary_table

  • Reads the input stream (single ended fastq) and reports the most frequent DNA fragments.
  • usable for QC of barcodes (sample barcodes, cellular barcode) in scRNA-seq
  • compiled with gcc >= 4.8.5
  • test usage:
gunzip -c data/test.R3.fq.gz | summary_table > data/test.R3.table.csv 2> messages.txt
head data/file.R3.table.csv
cat messages.txt
  • real usage:
gunzip -c real_huge.R3.fq.gz | head -n 40000000 | summary_table > real_huge.R3.table.csv 2> messages.txt
cat messages.txt
head real_huge.R3.table.csv
  • O2 usage:
sbatch summary_table.sh real_huge.R3.fq.gz
  • compilation: compile.sh summary_table.cpp. Result is summary_table binary.