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ChiRA extract (version 1.4.31)

File containing CRLs information:

Have genomic information?:

Selecet Yes if you have an annotation file and provide corresponding genomic fasta file

Annotations in GTF format:

Choose the source for the FASTA file:

Genomic FASTA file:

TPM cut-off:

Transcripts with less than this percentile TPMs will be discarded in the final output. [0-1.0]

Score cut-off:

Hybrids with less than this score will be discarded in the final output. [0-2.0]

Maximum number of bases allowed between the chimericsegments of a read:

Did you use single or split reference for alignment?:

Reference FASTA file:

Reference fasta file

Second reference FASTA file:

Second reference fasta file.

Hybridize chimeric loci?:

Turning this option on increases the run time of the tool significantly.

intarna_mode:

Enforce seed interaction?:

Number of inter-molecular base pairs within the seed region:

IntaRNA --seedBP parameter

Minimal unpaired probability (per sequence) a seed region may have:

IntaRNA --seedMinPu parameter

Compute accessibility profiles for interacting sequences?:

Sliding window size for accessibility computation:

IntaRNA --accW parameter

IntaRNA temperature parameter in Celsius to setup the VRNA energy parameters:

Summarize interactions at loci level?:

What it does

This tool extracts the best chimeric alignments for each read. User can optionally hybridize the loci where the chimeric arms are mapping to.

Inputs

Tabular file containing CRLs information

Annotation GTF file

Reference fasta files. Provide both in case of split reference.

If your alignments are merged at genomic level in previous step (chira merge), then provide a reference genomic fasta fille.

Output

Tabular file containing chimeras information