Run AmpliCDR3

Run name:
Email (optional):
Sequence/reads file: FASTA/FASTQ (compressed or uncompressed) without spaces, parenthesis or other special symbols in the name
If reads have been already de-multiplexed into separate files (one file per sample), you can pack them into a single .zip or .tar.gz format file and use it as input.
Max. 500 MB Download example


Or file URL:

Paired-end reads file (optional): FASTQ (compressed or uncompressed)
Max. 500 MB


Or file URL:

CDR3 region pattern:
Custom pattern in REGEX format to extract the CDR3 region from the TCR sequences.
If you choose a species, the internal pre-defined patterns will have priority respect to the custom one.

Choose species: Uses specific parameters and reference sequences for the selected species.

Amplicon data: It is very important to specify all the primer and tag sequences in 5'->3' sense.
Shortening primer sequences to 7-9 nts can increase the number of retrieved sequences (eg. GAGTGTCAT instead of GAGTGTCATTTCTCCAACGGGA).
Unique Molecular Identifier sequences (UMIs) must be indicated between parenthesis.


or file: Max. 100 KB See example


Alleles file (optional): FASTA format Max. 2 MB See example


Additional options:

Check reverse complementary: Checks the reverse complementary sequences if it fails to recognize the CDR3 region in the original orientation (it will double analysis time).
Number of reads to process: Maximum number of sequences/reads to be processed.
Number of UMIs to process: Maximum number of UMIs to be processed.
Remove singletons: Removes singletons (CDR3 variants with coverage 1).
Cluster CDR3 within UMIs: If at least half of the sequences within the same UMI cluster are similar (up to 2 substitutions), the consensus sequence is retrieved as a unique variant.
Cluster CDR3 errors: Groups together CDR3 sequences that differ in 1 or 2 substitutions. Use this option carefully because clusters may include several real CDR3 variants

Disclaimer

Your use of any of these tools is at your own risk. We do not give any representation or warranty nor assume any liability or responsibility for the data nor the results posted (whether as to their accuracy, completeness, quality or otherwise). Access to these data is available free of charge for ordinary use in the course of research. By visiting the site, you accept our use of cookies and you accept that your data and results will be stored in our server.