Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update PAF.md regarding the target interval #93

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Update PAF.md regarding the target interval #93

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
28 changes: 14 additions & 14 deletions PAF.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,20 +4,20 @@ PAF is a text format describing the approximate mapping positions between two
set of sequences. PAF is TAB-delimited with each line consisting of the
following predefined fields:

|Col|Type |Description |
|--:|:----:|:-----------------------------------------|
|1 |string|Query sequence name |
|2 |int |Query sequence length |
|3 |int |Query start (0-based; BED-like; closed) |
|4 |int |Query end (0-based; BED-like; open) |
|5 |char |Relative strand: "+" or "-" |
|6 |string|Target sequence name |
|7 |int |Target sequence length |
|8 |int |Target start on original strand (0-based) |
|9 |int |Target end on original strand (0-based) |
|10 |int |Number of residue matches |
|11 |int |Alignment block length |
|12 |int |Mapping quality (0-255; 255 for missing) |
|Col|Type |Description |
|--:|:----:|:-------------------------------------------------|
|1 |string|Query sequence name |
|2 |int |Query sequence length |
|3 |int |Query start (0-based; BED-like; closed) |
|4 |int |Query end (0-based; BED-like; open) |
|5 |char |Relative strand: "+" or "-" |
|6 |string|Target sequence name |
|7 |int |Target sequence length |
|8 |int |Target start on original strand (0-based; closed) |
|9 |int |Target end on original strand (0-based; open) |
|10 |int |Number of residue matches |
|11 |int |Alignment block length |
|12 |int |Mapping quality (0-255; 255 for missing) |

If PAF is generated from an alignment, column 10 equals the number of sequence
matches, and column 11 equals the total number of sequence matches, mismatches,
Expand Down