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immcantation / presto

pRESTO is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq). pRESTO is a bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
https://presto.readthedocs.io
GNU Affero General Public License v3.0
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AssemblePairs-reference : option to fill in nt from reference for gapped stitch #13

Closed ssnn-airr closed 8 years ago

ssnn-airr commented 9 years ago

Original report by Anonymous.

We talked about this option before (stealing sequence from reference when stitched reads do not overlap) but it occurred to me that it really makes even more sense for TCR stitching.

Low priority.

ssnn-airr commented 9 years ago

Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

Will add option to fill gap with reference sequence to AssemblePairs-reference. Maybe --fill?

ssnn-airr commented 8 years ago

Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

Yeah, it should probably come with a warning that you run the risk of making chimeric BCR sequences.

ssnn-airr commented 8 years ago

Original comment by Anonymous.

I am thinking this is particularly useful in TCR, and it would be good to be able to specify to fill-in for TCR but not BCR

ssnn-airr commented 8 years ago

Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

I added the --fill option to fill in the reference sequence. No extensive testing yet, but I checked several assemblies. Let me know if it's behaving for you.

ssnn-airr commented 8 years ago

Original comment by Anonymous.

wow ! i am super grateful. we will test.

PS you wouldn't be procrastinating on writing your thesis intro, would you !?!?!?

ssnn-airr commented 8 years ago

Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

No problem, and thanks.

PS: Maybe a little. At least it's Structured Procrastination...

ssnn-airr commented 8 years ago

Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

Seems to be working.