Analysis of single chain Fragment variable (scFv)

[d-jch]

Can mixcr analysis single chain Fragment variable (scFv) within which both V region of heavy and light chain are linked by a linker sequence.

[mizraelson]

Yes. If you can share a sample fastq file I will help with the command.

[d-jch]

sample.nanopore.fq.gz
Here is an sample fastq from a nanopore output, filtered by expected length (1000~1240)

[mizraelson]

Can you also share the linker sequence. I will use it to split two chains. Are there UMIs or other barcodes in the data?

[d-jch]

no UMIs or other barcodes, but some vector sequences

primer1: AGTAACGTTTGTCAGTAATTGCGGTTCTCACCC/GGGTGAGAACCGCAATTACTGACAAACGTTACT
primer2: CCCGCTGATCTGATAACAACAGTGTAGATGTAACAAAATCGAC/GTCGATTTTGTTACATCTACACTGTTGTTATCAGATCAGCGGG
linker : GCCGCCGCTGGAACTTGACCT/AGGTCAAGTTCCAGCGGCGGC

the IMGT/V-QUEST can do this, but not support large data~

[mizraelson]

Hi, can you please write to [email protected]
I will send you a custom solution