NAME

       ataqv - QC metrics for ATAC-seq data

DESCRIPTION

       ataqv 1.3.1: QC metrics for ATAC-seq data

       Usage:

       ataqv [options] organism alignment-file

   where:
              organism  is the subject of the experiment, which determines the list of autosomes (see "Reference
              Genome Configuration" below).

              alignment-file is a BAM file with duplicate reads marked.

       Basic options -------------

       --help: show this usage message.  --verbose: show more details and progress  updates.   --version:  print
       the  version  of  the  program.  --threads <n>: the maximum number of threads to use (right now, only for
       calculating TSS enrichment).

       Optional Input --------------

       --peak-file "file name"

              A BED file of peaks called for alignments in the BAM file. Specify "auto" to use the BAM file name
              with ".peaks" appended, or if the BAM file contains read groups, to assume each read group  has  a
              peak file whose name is the read group ID with ".peaks" appended. If you specify a single filename
              instead  of  "auto" with read groups, the same peaks will be used for all reads -- be sure this is
              what you want.

       --tss-file "file name"

              A BED file of transcription start sites for the experiment organism. If supplied, a TSS enrichment
              score will be calculated according to the ENCODE data standards.  This calculation  requires  that
              the BAM file of alignments be indexed.

       --tss-extension "size"

              If  a  TSS  enrichment  score  is requested, it will be calculated for a region of "size" bases to
              either side of transcription start sites. The default is 1000bp.

       --excluded-region-file "file name"

              A BED file containing excluded regions. Peaks or TSS overlapping these will be  ignored.   May  be
              given multiple times.

       Output ------

       --metrics-file "file name"

              The  JSON  file  to  which  metrics will be written. The default filename will be based on the BAM
              file, with the suffix ".ataqv.json".

       --log-problematic-reads

              If given, problematic reads will be logged to a file per read group, with names derived  from  the
              read  group IDs, with ".problems" appended. If no read groups are found, the reads will be written
              to one file named after the BAM file.

       --less-redundant

              If given, output a subset of metrics that should be less redundant. If this flag is used, the same
              flag should be passed to mkarv when making the viewer.

       Metadata --------

       The following options provide metadata to be included in the metrics JSON file.  They make it  easier  to
       compare results in the ataqv web interface.

       --name "name"

              A  label  to be used for the metrics when there are no read groups. If there are read groups, each
              will have its metrics named using its ID field. With no read groups  and  no  --name  given,  your
              metrics will be named after the alignment file.

       --ignore-read-groups

              Even  if  read  groups  are present in the BAM file, ignore them and combine metrics for all reads
              under a single sample and library named with the --name option. This also implies  that  a  single
              peak file will be used for all reads; see the --peak option.

       --nucleus-barcode-tag "nucleus_barcode_tag"

              Data  is  single-nucleus,  with the barcode stored in this BAM tag.  In this case, metrics will be
              collected per barcode.

       --description "description"

              A short description of the experiment.

       --url "URL"

              A URL for more detail on the experiment (perhaps using a DOI).

       --library-description "description"

              Use this description for all libraries in the BAM file, instead of using the DS  field  from  each
              read group.

       Reference Genome Configuration ------------------------------

       ataqv includes lists of autosomes for several organisms:

       Organism
              Autosomal References

       -------  ------------------

       fly    2R 2L 3R 3L 4

       human  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

       mouse  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19

       rat    1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

       worm   I II III IV V

       yeast  I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI

              The  default  autosomal  reference  lists  contain  names with "chr" prefixes ("chr1") and without
              ("1").  If  you  need  a  different   set   of   autosomes,   you   can   supply   a   list   with
              --autosomal-reference-file.

       --autosomal-reference-file "file name"

              A  file  containing  autosomal  reference  names, one per line. The names must match the reference
              names in the alignment file exactly, or the metrics based on counts of autosomal  alignments  will
              be wrong.

       --mitochondrial-reference-name "name"

              If  the  reference  name  for  mitochondrial  DNA in your alignment file is not "chrM",.  use this
              option to supply the correct name. Again, if this name is wrong, all  the  measurements  involving
              mitochondrial alignments will be wrong.

ataqv 1.3.1                                        April 2024                                           ATAQV(1)