Galaxy |

ChiRA merge (version 1.4.30)

Input BED file of alignments:

Do you have an annotation in GTF format?:

Annotations in GTF format:

Overlap fraction for merging mapped read positions to segments:

Matching read positions with greater than this fraction overlap are merged into a segment

Minimum length of the alignments as a fraction of longest:

Consider the alignments of a that read have at least longer than this value times the longest alignment for that read

Overlap fraction for merging alignments/blocks:

Minimum fraction of BED entries/blockbuster blocks that must overlap inorder to merge

Select the mode of merging:

Minimum locus size:

Minimum number of alignments to be present to output the merged a locus

Did you use single or split reference for alignment?:

chimeric_only:

What it does

This tool merges the overlapping aligned positions to define the read concentrated loci. If an annotation GTF file produced, the transcriptomic alignment positions are first converted to their corresponding genomic positions.

Inputs

Alignments in BED format
An annotation GTF file contaning reference genomic positions.

Output

BED file containing the alignments with reads categorized into segments depending on which part of the read is aligned.
Tabular file containing merged alignments. 4th column contains all the alignments merged into that location.