Paired end sequences and MiXCR.

qmarcou / IGoR

IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data. Find full documentation at:

https://qmarcou.github.io/IGoR/

GNU General Public License v3.0

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Paired end sequences and MiXCR. #30

Open poorvamudgal opened 6 years ago

poorvamudgal commented 6 years ago

Hi Quentin,

Can IGoR process paired end sequences? I didn't see this option in the manual input file section, see below,

Can be a fasta file, a csv file (with the sequence index as first column and the sequence in the second separated by a semicolon ';') or a text file with one sequence per line (format recognition is based on the file extension).

IGoR paper mentioned it can take grouped unique sequences from MiXCR, does that mean CDR3 sequences before clone assembly in MiXCR? Can you please enlighten more on this?

Thanks, Poorva

qmarcou commented 6 years ago

Hi Poorva, Sorry for the late reply I have been away with restricted access to the internet. IGoR can deal with paired end sequences like a char once the forward and backward reads have been merged. In order to obtain the most precise results you should define custom genomic offsets for V and (custom) reverse offsets for J so as to use your knowledge of the sequencing protocol at the alignment stage.

What 'grouped unique sequences' means is the fact that identical (or very close) sequences have been collapsed to a single sequence to control for PCR/sequencing errors and cell multiplicity.

Best, Quentin