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Convert BAM to ScIdx (version 1.0.1)

BAM file:

Require proper mate-pairing?:

Required if filtering by insert size for single-end Reqd 1 (below).

Read to output:

Minimum insert size to output:

Will not filter out single-end Read 1 unless proper mate-pairing is required (above).

Maximum insert size to output:

Will not filter out single-end Read 1 unless proper mate-pairing is required (above).

What it does

Converts BAM data to ScIdx, the Strand-specific coordinate count format, which is used by tools within the Chip-exo Galaxy flavor. ScIdx files are 1-based. The format consists of 5 columns: the chromosome, the position of the genomic coordinate, the number of tags on the forward strand, the number of tags on the reverse strand and the number of total tags on the position. With pair-end reads, only the 5’ end of READ1 will be used to create the ScIdx data file. Tools that use this format include GeneTrack and MultiGPS.

Options

Require proper mate-pairing? - Select Yes to require proper mate paring. Filtering by insert size parameters will not filter out single-end Read 1 unless proper mate-pairing is required.
Minimum insert size to output - Insert size below the minimum will be filtered from the results, but single-end Read 1 will not be filtered unless proper mate-pairing is required.
Maximum insert size to output - Insert size above the maximum will be filtered from the results, but single-end Read 1 will not be filtered unless proper mate-pairing is required.