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Output

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Ryan Wick edited this page Oct 15, 2015 · 1 revision

Bandage can output sequences to your computer's clipboard and to file. The various options are found in the 'Output' menu in Bandage's main menu bar.

Bandage can save sequence files in FASTA format and graph files in GFA format.

Copy selected node sequences to clipboard

This action will put the sequences for selected nodes in your computer's clipboard. Each node sequence is given its own line, and there are no headers.

Example:

GCCTTGACCACCGAAGCCGCCT
GGCGGCTTCGGTGGTCAAGGCGGC
GCCTTGACCACCGAAGCCGCCCTGACCACCGAAGCCGCCTTGA

This action can be completed using Ctrl+C (⌘+C on Mac).

Save selected node sequences to FASTA

This action will save a FASTA file containing the sequences for selected nodes. Each node sequence gets a header which contains the node name, length and read depth.

Example:

>NODE_512+_length_22_cov_107
GCCTTGACCACCGAAGCCGCCT
>NODE_513+_length_24_cov_170
GGCGGCTTCGGTGGTCAAGGCGGC
>NODE_811+_length_43_cov_52.0909
GCCTTGACCACCGAAGCCGCCCTGACCACCGAAGCCGCCTTGA

This action can be completed using Ctrl+S (⌘+S on Mac).

Copy selected path sequence to clipboard

This action will copy a single path sequence to the clipboard. It only works if the selected nodes form an unambiguous path through the graph. See Graph paths for more information.

Example:

GCCGCCTTGACCACCGAAGCCGCCTTGACCACCG

Save selected path sequence to FASTA

This action will save a path sequence to a FASTA file. The FASTA header will contain a comma-delimited list of the nodes in the path. It only works if the selected nodes form an unambiguous path through the graph. See Graph paths for more information.

Example:

>513-,512+,781-,106+,73+
GCCGCCTTGACCACCGAAGCCGCCTTGACCACCG

Specify exact path for copy/save

This action opens a window where you can specify more complex paths through the graph and then copy them to clipboard or save them to FASTA file. See Graph paths for more information.

Save entire graph to GFA

This action will save a GFA file of the entire graph. Even nodes and edges that are not currently visible will be included in the file. Nodes and edges that have been removed from the graph will not be included (see Editing graphs).

Save visible graph to GFA

This action will save a GFA file of the nodes and edges currently visible in the graph. Nodes and edges that have been hidden from the graph will not be included (see Editing graphs).

Example:

S	512	GCCTTGACCACCGAAGCCGCCT	LN:i:22	RC:i:2354
S	513	GGCGGCTTCGGTGGTCAAGGCGGC	LN:i:24	RC:i:4080
S	811	GCCTTGACCACCGAAGCCGCCCTGACCACCGAAGCCGCCTTGA	LN:i:43	RC:i:2240
L	513	-	512	+	21M
L	811	-	513	+	21M

Save entire graph to FASTA (both positive and negative nodes)

This action will save a FASTA file of all sequences in the graph – both positive node sequences and their reverse complement negative node sequences. This file will not contain any information about the graph edges.

Save entire graph to FASTA (only positive nodes)

This action will save a FASTA file of all positive node sequences in the graph but not their reverse complement negative node sequences. This file will be approximately half the size of the file generated by Save entire graph to FASTA (both positive and negative nodes) and is less redundant. It will not contain any information about the graph edges.

Web BLAST selected nodes

This action will open a browser to NCBI's BLAST web page, using the selected node sequences. See BLAST searches for more information.

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