notes.txt

##############################
Software requirements:
##############################

conda env with:
python 3.8
scipy
numpy
samtools #conda install -c bioconda samtools
datamash #conda install -c bioconda datamash
bedops #conda install -c bioconda bedops
ucsc-fetchchromsizes #conda install -c bioconda ucsc-fetchchromsizes
ucsc-wigtobigwig #conda install -c bioconda ucsc-wigtobigwig

Pacbio SMRT Link v10
# Download from https://www.pacb.com/support/software-downloads/
# install with smrtlink-*.run --rootdir smrtlink10 --smrttools-only


Scripts in src
Thresholds in config

##############################
Information on output:
##############################
02_ZMW_coords_per_chrom.sh:
$name.unique_ZMW_coords.tsv

$1: chrom
$2: start
$3: end
$4: ZMW_ID
$5: span
$6: subread coverage

03_Kinetics.sh:
tracks_m6A.$name.txt

$1: $chrom
$2: $chromStart
$3: $chromEnd
$4: $name
$5: $coverage
$6: $strand
$7: $thickStart
$8: $thickEnd
$9: $itemRgb
$10: $blockCount
$11: $blockSizes
$12: $blockStarts