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.