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Serghei Mangul edited this page Aug 7, 2017 · 2 revisions

Run ImReP analysis by a single command

python imrep.py --bam example/toyExample.bam example/toyExample.cdr3

Toy example with mapped and unmapped reads (.BAM) is provided in example directory.

On the screen the following informative message to appear:

Parse bam file with mapped and unmapped reads
Number of reads extacted from  IGH locus :  0
Number of reads extacted from  IGK locus :  0
Number of reads extacted from  IGL locus :  0
Number of reads extacted from  TRA locus :  0
Number of reads extacted from  TRB locus :  0
Number of reads extacted from  TRD locus :  0
Number of reads extacted from  TRG locus :  0
Number of unmapped reads extracted 100
Starting ImReP-0.6 (developped by Igor Mandric, Serghei Mangul)


 _                          
(_)_ __ ___  _ __ ___ _ __  
| | '_ ` _ \| '__/ _ \ '_ \ 
| | | | | | | | |  __/ |_) |
|_|_| |_| |_|_|  \___| .__/ 
                     |_|    


5 partial-V CDR3 found
0 partial-J CDR3 found
8 full CDR3 found:
	- 8 of type IGH
	- 0 of type IGK
	- 0 of type IGL
	- 0 of type TRA
	- 0 of type TRB
	- 0 of type TRD
	- 0 of type TRG
Done. Bye-bye

Results are in toyExample directory. This directory contains 2 files:

  • toyExample.cdr3 - assembled CDR3 sequences and corresponding VDJ recombinations
  • toyExample_onlyMapped_input.fasta - Reads prepared for ImReP analysis, composed of mapped reads from BCR/TCR loci (only soft clipped reads) and unmapped reads

We expect you to get the following CDR3 sequences saved in toyExample.cdr3

CDR3_AA_Seq	Chain_type	Read_count	V_chains	D_chains	J_chains
CAREGVVEYSSSSLALVCYYFDYW	IGH	4	IGHV3/OR16,IGHV1/OR15,IGHV3/OR1IGHD6	IGHJ4
CARDLVDIVATITVVLAEYFQHW	IGH	4	IGHV3/OR16,IGHV1/OR15,IGHV3/OR15	IGHD5	IGHJ4,IGHJ1
CARDTHVHGYSSGYRGYWYFDLW	IGH	17	IGHV3/OR16,IGHV1/OR15,IGHV3/OR15	IGHD6	IGHJ4,IGHJ2
CARLGTTGTTSGVSYFDYW	IGH	13	IGHV3/OR16,IGHV1/OR15,IGHV3/OR15	IGHD1	IGHJ4
CTRHVDTAMVTTYYYYYYYMDVW	IGH	18	IGHV3/OR16,IGHV1/OR15,IGHV3/OR15	IGHD5	IGHJ6,IGHJ4
CARGPTGITGTTNYYYYYGMDVW	IGH	21	IGHV3/OR16,IGHV1/OR15,IGHV3/OR15	IGHD1,IGHD1/OR15	IGHJ6
CARADVLAFLERLLYRFSTYYFDYW	IGH	2	IGHV3/OR16,IGHV1/OR15,IGHV3/OR1NA	IGHJ4
CVRGVVIGITGTTGRGEDYFDYW	IGH	13	IGHV3/OR16,IGHV1/OR15,IGHV3/OR15	IGHD1,IGHD1/OR15	IGHJ4,IGHJ3
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