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

doc: improved explanation of metadata TSV formatting for multiple barcodes #46

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

doc: improved explanation of metadata TSV formatting for multiple barcodes #46

Show file tree
Hide file tree
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
10 changes: 8 additions & 2 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -52,8 +52,14 @@ and placed in the given SAM record tag (`RX` by default). Similarly, the sample
barcode bases from the given read will be placed in the `BC` tag.

Metadata about the samples should be given as a headered metadata TSV file with
two columns 1. `sample_id` - the id of the sample or library. 2. `barcode` - the
expected barcode sequence associated with the `sample_id`.
at least the following two columns present:

1. `sample_id` - the id of the sample or library.
2. `barcode` - the expected barcode sequence associated with the `sample_id`.

For reads containing multiple barcodes (such as dual-indexed reads), all barcodes
should be concatenated together in the order they are read and stored in the
`barcode` field.

The read structures will be used to extract the observed sample barcode, template
bases, and molecular identifiers from each read. The observed sample barcode
Expand Down
9 changes: 7 additions & 2 deletions src/bin/commands/demux.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -518,9 +518,14 @@ impl DemuxMetric {
/// default). Similarly, the sample barcode bases from the given read will be placed in the `BC`
/// tag.
///
/// Metadata about the samples should be given as a headered metadata TSV file with two columns
/// 1. `sample_id` - the id of the sample or library.
/// Metadata about the samples should be given as a headered metadata TSV file with at least the
/// following two columns present:
///
/// 1. `sample_id` - the id of the sample or library.
/// 2. `barcode` - the expected barcode sequence associated with the `sample_id`.
///
/// For reads containing multiple barcodes (such as dual-indexed reads), all barcodes should be
/// concatenated together in the order they are read and stored in the `barcode` field.
///
/// The read structures will be used to extract the observed sample barcode, template bases, and
/// molecular identifiers from each read. The observed sample barcode will be matched to the
Expand Down
Loading