Galaxy |

ChiRA map (version 1.4.30)

Input FASTA file:

Input fasta file

Single or split reference?:

Use single if you have all the transcripts in single fasta file. Use split, if you split the reference into two such that each chimeric read arm corresponds to one of them

Reference FASTA file:

Reference fasta file

Second reference FASTA file:

Second reference fasta file.

aligner:

Map reads to:

Seed length 1:

Seed length for 1st mapping iteration. bwa-mem parameter -k

Seed length 2:

Seed length for 2nd mapping iteration. bwa-mem parameter -k

Minimum alignmnet score for 1st mapping iteration:

bwa-mem parameter '-T'

Minimum alignmnet score for 2nd mapping iteration:

bwa-mem parameter '-T'

Matching score for 1st mapping iteration:

Mismatch penalty for 1st mapping iteration:

Matching score for 2nd mapping iteration:

Mismatch penalty for 2nd mapping iteration:

Gap opening penalty for 1st mapping iteration:

Gap extension penalty for 1st mapping iteration:

Gap opening penalty for 2nd mapping iteration:

Gap extension penalty for 2nd mapping iteration:

Maximum number of allowed multi hits per read in 1st iteration:

Maximum number of allowed multi hits per read in 2nd iteration:

What it does

This tool handles the mapping of the reads to reference transcriptome. User can choose between the bwa-mem and CLAN alignment tools.

Inputs

A fasta file containing reads
A reference fasta file containing transcript sequences
An optional second reference fasta file, incase if you split your reference into two

Output

BED file containing the alignments
unmapped FASTA file (only for aligner BWA-MEM)