notes

python ~/GITHUB/indrops/indrops.py project.yaml filter

python ~/GITHUB/indrops/indrops.py project.yaml identify_abundant_barcodes

python ~/GITHUB/indrops/extract_barcoded_reads.py project.yaml sort

python ~/GITHUB/indrops/extract_barcoded_reads.py project.yaml quantify --no-bam > barcoded_reads.fastq



## note, must make the read name unique:

encode_read_number_in_fastq.pl barcoded_reads.fastq > barcoded_reads.adj.fq

# align reads to target transcripts using bowtie:

bowtie target.fasta.bowtie -q -p 20 -a --best --strata --chunkmbs 1000 --sam -m 200 -n 1 -l 15 -e 100 barcoded_reads.adj.fq  >  target.bowtie.adj.sam


# generate count matrix:

bam_to_count_matrix.pl --bam target.bowtie.adj.sam > sc.counts.matrix