Galaxy |

CollectBaseDistributionByCycle (version 3.1.1.0)

Select SAM/BAM dataset or dataset collection:

If empty, upload or import a SAM/BAM dataset.

Load reference genome from:

Using reference genome:

REFERENCE_SEQUENCE

Calculate the base distribution over aligned reads only:

ALIGNED_READS_ONLY

Calculate the base distribution over PF (passing filtering) reads only:

PF_READS_ONLY

Assume the input file is already sorted:

ASSUME_SORTED

Select validation stringency:

Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.

Purpose

Program to chart the nucleotide distribution per cycle in a SAM or BAM file.

Dataset collections - processing large numbers of datasets at once

This will be added shortly

Inputs, outputs, and parameters

Either a SAM file or a BAM file must be supplied. Galaxy automatically coordinate-sorts all uploaded BAM files.

From Picard documentation( http://broadinstitute.github.io/picard/):

ALIGNED_READS_ONLY=Boolean    If set to true, calculate the base distribution over aligned reads only.  Default value:
                              false. This option can be set to 'null' to clear the default value. Possible values:
                              {true, false}

PF_READS_ONLY=Boolean         If set to true calculate the base distribution over PF reads only.  Default value: false.
                              This option can be set to 'null' to clear the default value. Possible values: {true,
                              false}

REFERENCE_SEQUENCE=File
R=File                        Reference sequence fasta  Default value: null.

ASSUME_SORTED=Boolean
AS=Boolean                    If true (default), then the sort order in the header file will be ignored.  Default

Additional information

Additional information about Picard tools is available from Picard web site at http://broadinstitute.github.io/picard/ .