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Barracoda 1.8 Server

A tool for analysing DNA barcode sequencing data.

Andrea M. Marquard and Aron C. Eklund

Instructions Output format Article abstract


Sequencing data (explain)

Submit FASTA/FASTQ file:   

Barcode information (explain)

For each tag within the barcode, either submit a FASTA file of expected sequences, or paste the sequence if there is only one, or type the expected base pair length if the sequence is unknown.
Orientation: Sequences should be oriented according to the orientation of the individual A- and B-oligos before annealing. Ie., B-sequences should be the reverse complement of what is expected in the sequencing reads.

Sample identification tag     (select FASTA file)
Forward primer A (paste sequence)
N sequence (type length of tag)
Epitope tag A (select FASTA file)
Annealing region (paste sequence)
Epitope tag B (select FASTA file)
N sequence (type length of tag)
Forward primer B (paste sequence)

Sample identification (explain)

Upload a tab-delimited file of paired sequence IDs (1st column) and sample names (2nd column). The file should contain no headers.
The sequence IDs should be the same as those found in the Sample identification tag FASTA file uploaded above.
Make sure to use identical names for replicates, and call your baseline samples "input" (no capital letters)

Sample identification table   

Barcode annotations (explain)

Upload a file with annotations for the barcodes (text file or Excel workbook)
If your fastq file contains multiple experiments with different annotation files, use an Excel workbook and add the annotations as different sheets (read more). There should be a column with MHC allele details.
***NEW!*** Log fold change and p-values are now automatically calculated for full libraries and for MHC alleles individually.

Barcode annotations   

Barcode plate setup (optional) (explain)

Upload an excel file with the experimental plate setup of the barcodes. Include as many plates as possible (also if you didn't use them), to make sure you detect any cross-plate contamination.

Barcode plate setups   


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