Commit e4e9de97 authored by flothoni's avatar flothoni Committed by Mathieu Giraud

IKFZ1: rename IKAROS occurences by IKZF1

parent 98a28d86
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens-ikaros.g -r 1 -e 0.1 $VIDJIL_DATA/ikaros_debre.fa
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens-isoforms.g -r 1 -e 0.1 $VIDJIL_DATA/ikaros_debre.fa
$ All sequences have been seen as different IKAROS recombinations
$ All sequences have been seen as different IKZF1 recombinations
1: found 22 windows in 22 reads
1: IKAROS .* -> .* 22
1: IKZF1 .* -> .* 22
### control sequence given by Debré ###
# del4-7__jonction_intron3_intron7
$ Find the correct assignation for the sequence IKAROS-INTRON-3//IKAROS-INTRON-7
1: IKAROS-INTRON-3 16/CCCGCG/8 IKAROS-INTRON-7
$ Find the correct assignation for the sequence IKZF1-INTRON-3//IKZF1-INTRON-7
1: IKZF1-INTRON-3 16/CCCGCG/8 IKZF1-INTRON-7
# del2-7__jonction_intron1_var_intron7
$ Find the correct assignation for the sequence IKAROS-INTRON-1-var//IKAROS-INTRON-7
1: IKAROS-INTRON-1-var 26/CC/14 IKAROS-INTRON-7
$ Find the correct assignation for the sequence IKZF1-INTRON-1-var//IKZF1-INTRON-7
1: IKZF1-INTRON-1-var 26/CC/14 IKZF1-INTRON-7
# del4-8__jonction_intron3_3UTR (could also be IKAROS-INTRON-3 1/GG/5 3'UTR_breakpoint1).
$ Find the correct assignation for the sequence IKAROS-INTRON-3//3_UTR
1: IKAROS-INTRON-3 1//3 IKAROS-3'UTR-breakpoint1
# del4-8__jonction_intron3_3UTR (could also be IKZF1-INTRON-3 1/GG/5 3'UTR_breakpoint1).
$ Find the correct assignation for the sequence IKZF1-INTRON-3//IKZF1-INTRON-8
1: IKZF1-INTRON-3 1//3 IKZF1-INTRON-8
# del2-8__jonction_intron1_3UTR
$ Find the correct assignation for the sequence IKAROS-INTRON-1//3_UTR
1: IKAROS-INTRON-1 18/TTCTAA/9 IKAROS-3'UTR-breakpoint1
$ Find the correct assignation for the sequence IKZF1-INTRON-1//IKZF1-INTRON-8
1: IKZF1-INTRON-1 18/TTCTAA/9 IKZF1-INTRON-8
### cas patient 19498 ###
$ Find the correct assignation for the sequence
1: IKAROS-INTRON-3 2/TT/3 IKAROS-INTRON-7
1: IKZF1-INTRON-3 2/TT/3 IKZF1-INTRON-7
$ Find the correct assignation for the sequence
1: IKAROS-INTRON-3 2/GAA/2 IKAROS-INTRON-7
1: IKZF1-INTRON-3 2/GAA/2 IKZF1-INTRON-7
$ Find the correct assignation for the sequence
1: IKAROS-INTRON-3 7/TCGAGG/5 IKAROS-INTRON-7
1: IKZF1-INTRON-3 7/TCGAGG/5 IKZF1-INTRON-7
### 13922 - sequences ikfz1 ####
$ Find the correct assignation for the sequence (témoin del4-7)
1: IKAROS-INTRON-3 1//2 IKAROS-INTRON-7
1: IKZF1-INTRON-3 1//2 IKZF1-INTRON-7
$ Find the correct assignation for the sequence (témoin del2-7)
1: IKAROS-INTRON-1 8/CCCTTC/3 IKAROS-INTRON-7
1: IKZF1-INTRON-1 8/CCCTTC/3 IKZF1-INTRON-7
$ Find the correct assignation for the sequence (seq 4-7 du patient)
1: IKAROS-INTRON-3 0/TCGG/6 IKAROS-INTRON-7
1: IKZF1-INTRON-3 0/TCGG/6 IKZF1-INTRON-7
### 17464 - sequences ikfz1 ####
$ Find the correct assignation for the sequence (del4-7 majo)
1: IKAROS-INTRON-3 5/GA/2 IKAROS-INTRON-7
1: IKZF1-INTRON-3 5/GA/2 IKZF1-INTRON-7
$ Find the correct assignation for the sequence
1: IKAROS-INTRON-3 1/TC/2 IKAROS-INTRON-7
1: IKZF1-INTRON-3 1/TC/2 IKZF1-INTRON-7
$ Find the correct assignation for the sequence
1: IKAROS-INTRON-3 5/CGGGCG/16 IKAROS-INTRON-7
1: IKZF1-INTRON-3 5/CGGGCG/16 IKZF1-INTRON-7
$ Find the correct assignation for the sequence
1: IKAROS-INTRON-3 0/C/3 IKAROS-INTRON-7
1: IKZF1-INTRON-3 0/C/3 IKZF1-INTRON-7
$ Find the correct assignation for the sequence
1: IKAROS-INTRON-3 3/GCGG/5 IKAROS-INTRON-7
1: IKZF1-INTRON-3 3/GCGG/5 IKZF1-INTRON-7
$ Find the correct assignation for the sequence
1: IKAROS-INTRON-3 1/GGTTAAAG/5 IKAROS-INTRON-7
1: IKZF1-INTRON-3 1/GGTTAAAG/5 IKZF1-INTRON-7
### 13444 - sequences ikfz1 ####
$ Find the correct assignation for the sequence (del4-7 majo 1)
1: IKAROS-INTRON-3 1/GCCTCC/2 IKAROS-INTRON-7
1: IKZF1-INTRON-3 1/GCCTCC/2 IKZF1-INTRON-7
$ Find the correct assignation for the sequence (del4-7 majo 4)
1: IKAROS-INTRON-3 0/C/2 IKAROS-INTRON-7
1: IKZF1-INTRON-3 0/C/2 IKZF1-INTRON-7
$ Find the correct assignation for the sequence (del4-7 majo 3)
1: IKAROS-INTRON-3 1/TAGG/6 IKAROS-INTRON-7
1: IKZF1-INTRON-3 1/TAGG/6 IKZF1-INTRON-7
$ Find the correct assignation for the sequence (del4-7 majo 2)
1: IKAROS-INTRON-3 7/TCGGT/3 IKAROS-INTRON-7
1: IKZF1-INTRON-3 7/TCGGT/3 IKZF1-INTRON-7
$ Find the correct assignation for the sequence (del2-7 majo)
1: IKAROS-INTRON-1 5//3 IKAROS-INTRON-7
1: IKZF1-INTRON-1 5//3 IKZF1-INTRON-7
$ Find the correct assignation for the sequence (del2-7 mino)
1: IKAROS-INTRON-1 8/CCGA/3 IKAROS-INTRON-7
1: IKZF1-INTRON-1 8/CCGA/3 IKZF1-INTRON-7
......@@ -8,13 +8,13 @@
"systems": {
"IKAROS": {
"IKZF1": {
"shortcut": "I",
"color" : "#d63a19",
"description": "IKAROS Trsl locus",
"recombinations": [ {
"5": ["IKAROS-as-V.fa"],
"3": ["IKAROS-as-J.fa"]
"5": ["IKZF1-as-V.fa"],
"3": ["IKZF1-as-J.fa"]
} ],
"parameters": {
"seed": "10s"
......
>IKAROS-INTRON-7
>IKZF1-INTRON-7
tggaaacatcaagtctagtgtaactgtttcttcttcaaggtgatttgcattttattccTGAATGCCTGAGGGTTCTTT
>IKAROS-3'UTR-breakpoint1
>IKZF1-INTRON-8
caaggtgtgggctgacatgctggctctcttccctgtatgccgagacatgcttgggatctcctagctccacactctgtctctcatgagtctgagccctttgggTTTCTGTGACTTCCAGTCCCC
>IKAROS-3'UTR-breakpoint2
>IKZF1-3'UTR-breakpoint2
cctgcagcacagtgtgtttctttctttccccacatcaagggtctacgtggaatagtgcttttccacagagtagctactagccacacatggctatttcaatttacattataatgaaatagaattgaaacttcagcccttcagttgtactagccatattccaggtgttctatcagcagatgtgactgtacccaccatattggacagcacaaatgtggaagcagacgtttccattgttgtagaaggctctgtcgggaagtgctgatgacatgccagtacctgccttgctccctggagctccccaaggtctagcacagtgcctggcacaaggtgaggggggtgcccagaaaagattcaattccctctccaagtaaaccattcattcccagcttccccaaagaagtcttccctggggtactaaatcctgaaggctgccttcagtattcgaagcatgcagcaactttcacttcttctttttcgacctggcccttcactctgcctgagagggaaatgtcacttgcctgaggacatgtgctttttctcaagcaggcacactggtccctttcaaggtgtgggctgacatgctggctctcttccctgtatgccgagacatgcttgggatctcctagctccacactctgtctctcatgagtctgagccctttgggTTTCTGTGACTTCCAGTCCCC
>IKAROS-INTRON-1-var
>IKZF1-INTRON-1-var
CAAACACTTCAAGATTATGCATTTattaacagatacatgaaataaattccatgtgcatatgcacatatgcacacagagcgtgcacacacacagcatgcacacagcgtggagtgagaggcatggggcagtgtggaagagttttaacatcaaacagacctgaaatgagtattaaaggccccctttatttttaaacttttactaaaacaagatggatttccctatgttatataatggtgaattttaggcataaataacgttttttgagtgttgcataattgtacgtattaatgtaatgtaactgtggttaacgaagaattcatcaaggatatcactgttttgtggcattttttttttcctcctctaatctttggacttgtgaaataatttcactatgaaataaatgttggttcttgtcatattctaagggagattgatgtaagtggctccactccagcttacagaaggtaaaccacgacctttttgcgttc
>IKAROS-INTRON-1
>IKZF1-INTRON-1
CAACAAGTGACCCATCCTTTGaagcttacaagaagagaaacattaatctatttcacgtcttgaaaacagatcagttttattttgctcaaaaagggcacatgtacatttttgatctaggtcttagaaacgtagagtttcagaggatcagcattatacac
>IKAROS-INTRON-3
>IKZF1-INTRON-3
TGTGAAGGTCACACCCTCTGgtcttctcccagcccatagggtataaataatctgaattgacggcatccagggatctcagaaattattagtacatccc
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