FR1, FR2, FR3, FR4 Fragments of the BCR

liulab-dfci / TRUST4

TCR and BCR assembly from RNA-seq data

MIT License

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FR1, FR2, FR3, FR4 Fragments of the BCR #15

Open tAndreani opened 4 years ago

tAndreani commented 4 years ago

Hello,

i am wondering if it is possible to have in the final annotation file also the other regions of the BCRs such as FR1, FR2, FR3, FR4.. I can see from the trust_cdr3.out there are the CDR1 CDR2 and CDR3 but what about the fragments in between them?

mourisl commented 4 years ago

That information is in the trust_annot.fa output. Each description line has the annotation for a BCR/TCR assembly, and the format is described in the README file. FR1...4 information can be inferred from the coordinates of V, J genes and CDR1...3. I can write a script to help reformat this annotation file.

tAndreani commented 4 years ago

Yea that would be very helpful. Am sorry but is not very intuitive how to get FR1, FR2 from the all the files in the output of TRUST4 etc.. In the README I have checked and are reported the CDR1, CDR2, CDR3 sequences but not the FR1, FR2 etc..