Published Workflows | r-mauleon | Test-Liftover from Nipp genome to IR8-3

Galaxy Workflow ' Test-Liftover from Nipp genome to IR8-3'

Step 1: Input dataset
select at runtime
The coordinate file (3 column format : contigstartend of the genome location in source genome.
Step 2: Batch-get-subseq
Nipponbare reference 1.0
Output dataset 'output' from step 1
3 column tab delimited: chrName start stop
This gets the (multi)FASTA file sequence(s) from the source genome.
Step 3: Find-seq
Output dataset 'output' from step 2
IR 8

No value found for 'maximum gap between tiles in a clump', used default

Default blat tabular format,no sequence
The (multi)FASTA file from source genome is aligned to the target genome.
Step 4: Cut
Output dataset 'output' from step 3
PSL postprocessing step to parse out cols 14,16,17 , the alignment coordinates.
Step 5: Remove beginning
Output dataset 'out_file1' from step 4
removes the 1st 5 lines of the header of the alignment output
Step 6: Batch-get-subseq
IR 8
Output dataset 'out_file1' from step 5
3 column tab delimited: chrName start stop
Extracts the equivalent/lifted-over (mult) FASTA from the target genome.