Galaxy | Published Workflow | Bam to Fasta

Bam to Fasta

Annotation:

Step	Annotation
Step 1: BAM to BED Convert the following BAM file to BED select at runtime What type of BED output would you like Create a 6-column BED file Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage. False Use alignment's edit-distance for BED score False Use other NUMERIC BAM alignment tag as the BED score Empty.
Step 2: MergeBED Sort the following BAM/BED/VCF/GFF file Output dataset 'output' from step 1 Calculation based on strandedness? Overlaps on either strand Maximum distance between features allowed for features to be merged 0 Print the header from the A file prior to results False Applying operations to columns from merged intervals
Step 3: GetFastaBed BED/VCF/GFF file Output dataset 'output' from step 2 Choose the source for the fasta file History Fasta file select at runtime Use the 'name' column in the BED file for the FASTA headers in the output FASTA file False Report extract sequences in a tab-delimited format instead of in FASTA format False Force strandedness False Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage. False

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antunderwood

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