Commit a05819e0 authored by Mathieu Giraud's avatar Mathieu Giraud

Merge branch 'feature-a/3008-default_J_downstream' into 'dev'

Feature a/3008 default j downstream

See merge request !148
parents 751992b2 edd001ee
Pipeline #33011 passed with stages
in 45 minutes and 37 seconds
...@@ -2,17 +2,17 @@ ...@@ -2,17 +2,17 @@
# one half is first 60 bp of some V genes # one half is first 60 bp of some V genes
# the other half is a 40 bp di-mer sequence # the other half is a 40 bp di-mer sequence
>TRAV1-1*01--cgcg >TRAV1-1*01--caca
ggacaaagccttgagcagccctctgaagtgacagctgtggaaggagccattgtccagata ggacaaagccttgagcagccctctgaagtgacagctgtggaaggagccattgtccagata
cgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcg cacacacacacacacacacacacacacacacacacacaca
>TRGV1*01--cgcg >TRGV1*01--caca
tcttccaacttggaagggagaacgaagtcagtcaccaggctgactgggtcatctgctgaa tcttccaacttggaagggagaacgaagtcagtcaccaggctgactgggtcatctgctgaa
cgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcg cacacacacacacacacacacacacacacacacacacaca
>IGHV1-18*01--cgcg >IGHV1-18*01--caca
caggttcagctggtgcagtctggagctgaggtgaagaagcctggggcctcagtgaaggtc caggttcagctggtgcagtctggagctgaggtgaagaagcctggggcctcagtgaaggtc
cgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcg cacacacacacacacacacacacacacacacacacacaca
>atat--TRBV1*01 >atat--TRBV1*01
......
...@@ -3,7 +3,7 @@ ...@@ -3,7 +3,7 @@
# Sequences outside any V(D)J locus # Sequences outside any V(D)J locus
>too_few_vj-1 >too_few_vj-1
CTAGGCATGGCTCCTCTCCACAGGAAAACTCCACTCCAGTGCTCAGCTTGCACCCTGGCACAGGCCAGCAGTTGCTGGAAGTCAGACACCTGAGAAGAAC CTAGGCATGGCTCCTCTCCACAGGAAAACTCCACTCCAGTGCTCAGCTTGCACCCTGGCACAGGCCAGCAGTTGCTGGAAGTCAGACACCTGTGAAGAAC
>too_few_vj-2 >too_few_vj-2
GCCTCAGGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCGCACAGTGCTGGTTCCGTCACCCCCACCCAGGGAAGCAGGTCTGAGCAGCTTGTCCTGGCTG GCCTCAGGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCGCACAGTGCTGGTTCCGTCACCCCCACCCAGGGAAGCAGGTCTGAGCAGCTTGTCCTGGCTG
......
...@@ -7,7 +7,7 @@ $ The FineSegmenter gives the locus information (-2) ...@@ -7,7 +7,7 @@ $ The FineSegmenter gives the locus information (-2)
1:Unexpected [+]TRBV/[+]TRGJ 1:Unexpected [+]TRBV/[+]TRGJ
1:Unexpected [+]TRDV/[+]IGHJ 1:Unexpected [+]TRDV/[+]IGHJ
1:Unexpected [+]TRDV/[-]IGKV 1:Unexpected [+]TRDV/[-]IGKV
1:Unexpected [-]IGLJ/[+]TRGJ 1:Unexpected [-]IGLJ.down/[+]TRGJ
$ The FineSegmenter gives the locus information (-2) and takes the best strand $ The FineSegmenter gives the locus information (-2) and takes the best strand
1:Unexpected [+]IGKV/[+]IGLJ 1:Unexpected [+]IGKV/[+]IGLJ
......
...@@ -4,14 +4,14 @@ $ number of reads and kmers ...@@ -4,14 +4,14 @@ $ number of reads and kmers
1:13153 reads, 3020179 kmers 1:13153 reads, 3020179 kmers
$ k-mers, IGHV $ k-mers, IGHV
1:13115 .* 1222984 .*IGHV 1:13116 .* 1219953 .*IGHV
$ k-mers, IGHJ $ k-mers, IGHJ
1:38 .* 435867 .*IGHJ 1:37 .* 435550 .*IGHJ
$ k-mers, ambiguous $ k-mers, ambiguous
1:47648 .*\\? 1:53426 .*\\?
$ k-mers, unknown $ k-mers, unknown
1:1251567 .*_ 1:1248938 .*_
...@@ -10,7 +10,7 @@ CTACTACTACATGGACGTCTGGGGCAAAGGGACCCTGGTCACCGTCTCCTCAGGT ...@@ -10,7 +10,7 @@ CTACTACTACATGGACGTCTGGGGCAAAGGGACCCTGGTCACCGTCTCCTCAGGT
>TRGV2*01 1/C/0 TRGJ1*02 [TRG] {CATWDG!YYKKLF} >TRGV2*01 1/C/0 TRGJ1*02 [TRG] {CATWDG!YYKKLF}
GGAAGGCCCCACAGCGTCTTCAGTACTATGACTCCTACAACTCCAAGGTTGTGTTGGAATCAGGAGTCAGTCCAGGGAAGTATTATACTTACGCAAGCACAAGGAACAACTTGAGATTGATACTGCGAAATCTAATTGAAAATGACTCTGGGGTCTATTACTGTGCCACCTGGGACGGCTTATTATAAGAAACTCTTTGGCAGTGGAACAACAC GGAAGGCCCCACAGCGTCTTCAGTACTATGACTCCTACAACTCCAAGGTTGTGTTGGAATCAGGAGTCAGTCCAGGGAAGTATTATACTTACGCAAGCACAAGGAACAACTTGAGATTGATACTGCGAAATCTAATTGAAAATGACTCTGGGGTCTATTACTGTGCCACCTGGGACGGCTTATTATAAGAAACTCTTTGGCAGTGGAACAACAC
>TRGV3*01 0/CC/0 TRGJ1*01 [TRG] {CATWDRPNYYKKLF} >TRGV3*01 0/CC/0 (TRGJ1*01, TRGJ2*01) [TRG] {CATWDRPNYYKKLF}
GGAAGGCCCCACAGCGTCTTCTGTACTATGACGTCTCCACCGCAAGGGATGTGTTGGAATCAGGACTCAGTCCAGGAAAGTATTATACTCATACACCCAGGAGGTGGAGCTGGATATTGAGACTGCAAAATCTAATTGAAAATGATTCTGGGGTCTATTACTGTGCCACCTGGGACAGGCCGAATTATTATAAGAAACTCTTTGGCAGTGGAACAACAC GGAAGGCCCCACAGCGTCTTCTGTACTATGACGTCTCCACCGCAAGGGATGTGTTGGAATCAGGACTCAGTCCAGGAAAGTATTATACTCATACACCCAGGAGGTGGAGCTGGATATTGAGACTGCAAAATCTAATTGAAAATGATTCTGGGGTCTATTACTGTGCCACCTGGGACAGGCCGAATTATTATAAGAAACTCTTTGGCAGTGGAACAACAC
# PCR dimer (V4-K5), should not be segmented # PCR dimer (V4-K5), should not be segmented
# #
>dimer__UNSEG >dimer [unexpected]
GAGCTCTGTGACCGCCGCGGACACGACTGGAGATTAAACGTAAGTGTAGAACCATGTCGTCAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAA GAGCTCTGTGACCGCCGCGGACACGACTGGAGATTAAACGTAAGTGTAGAACCATGTCGTCAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAA
>IGKV1-5*03 9/4/1 IGKJ1*01 [IGK] {CQQYNRLWTF} >IGKV1-5*03 (9/4/1 IGKJ1*01, 9/7/4 IGKJ4*02) [IGK] {CQQYNRLWTF}
CTCCTGCTACTCTGGCTCCCAGGTGCCAAATGTGACATCCAGATGACCCAGTCTCCTTCCACCCTGTCTGCGTCTGTAGGAGACAGAGTCACCATCACCTGCCGGGCCAGTCAGAGTATTAATAACAACTTGGCCTGGTATCAGGAGAAGCCAGGGAAAGCCCCTAAGGTCCTGATCTATAAGGCGTCTAGTTTAGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGAATTCACTCTCACCATCAGCAGCCTGCAGCCTGATGATTTTGCAACCTATTACTGCCAACAATATAATAGACTTTGGACGTTCGGCCAAGGGACCAAGGTGGAAGTCAAACGAACTGTGGCTGCACCATCT CTCCTGCTACTCTGGCTCCCAGGTGCCAAATGTGACATCCAGATGACCCAGTCTCCTTCCACCCTGTCTGCGTCTGTAGGAGACAGAGTCACCATCACCTGCCGGGCCAGTCAGAGTATTAATAACAACTTGGCCTGGTATCAGGAGAAGCCAGGGAAAGCCCCTAAGGTCCTGATCTATAAGGCGTCTAGTTTAGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGAATTCACTCTCACCATCAGCAGCCTGCAGCCTGATGATTTTGCAACCTATTACTGCCAACAATATAATAGACTTTGGACGTTCGGCCAAGGGACCAAGGTGGAAGTCAAACGAACTGTGGCTGCACCATCT
# TRGV3*01 TGCCACCTGGGACAGG
# |||||||||||||
# seq GGGGTCTATTACTGTGCCACCTGGGACTCTTCTGTTGTCACAGGTAAGTATC
# ||.||.|| .|||.||....|||||||||||||||||||||
# TRGJ2*01 GAATTATTATAAGAAACTCTTTGGCA GTGGAACAACACTTGTTGTCACAGGTAAGTATC
# ^ ^ ^
# 0 18 37
>TRGV3*01 3/TCTTC/39 TRGJ2*01 [TRG] BUG
CTACACCAGGAGGGGAAGGCCCCACAGCGTCTTCTGTACTATGACGTCTACACCGCAAGGGATGTGTTGGAATCAGGACTCAGTCCAGGAAAGTATTATACTCATACACCAAGGAGGTGGAGCTGGATATTGAGACTGCAAAATCTAATTGAAAATGATTCTGGGGTCTATTACTGTGCCACCTGGGAC
TCTTC
TGTTGTCACAGGTAAGTATCGGAAGAAT
\ No newline at end of file
...@@ -8,7 +8,8 @@ tccccctgatcctggagtcgcccagccccaaccagacccaaag ...@@ -8,7 +8,8 @@ tccccctgatcctggagtcgcccagccccaaccagacccaaag
ctacgagcagtacttcgggccgggcaccaggctcacggttacaggtaag ctacgagcagtacttcgggccgggcaccaggctcacggttacaggtaag
#target 0447GG #target 0447GG
>TRBD2*02 1/AATG/0 TRBJ2-3*01 [TRB+] BUG #See #3145, this sequence may be a TRBJ2-2 ... TRBD2 ... TRBJ2-3 !
>TRBD2*02 1/AATG/0 TRBJ2-3*01 [TRB+] TODO
CAGGGCTGAGCGAACACCGGGGAGCTGTTTTTTGGAGAAGGCTCTAGGCTGACCGTACTGGGTAAGGAGGCG CAGGGCTGAGCGAACACCGGGGAGCTGTTTTTTGGAGAAGGCTCTAGGCTGACCGTACTGGGTAAGGAGGCG
GTTGGGGCTCCGGAGAGCTCCGAGAGGGCGGGATGGGCAGAGGTAAGCAGCTGCCCCACTCTGAGAGGGGCT GTTGGGGCTCCGGAGAGCTCCGAGAGGGCGGGATGGGCAGAGGTAAGCAGCTGCCCCACTCTGAGAGGGGCT
GTGCTGAGAGGTTTTTCCAAGCCCCACACAGTCAGACTAACCTCTGCCACCTGCGCTTCCTGCCGCTGCCCA GTGCTGAGAGGTTTTTCCAAGCCCCACACAGTCAGACTAACCTCTGCCACCTGCGCTTCCTGCCGCTGCCCA
......
...@@ -10,8 +10,8 @@ TGCCGGGCAGTCAGGGCATTAGAAATGATTTAGGCTGGTATCAGCAGAAACCAGGGNAAAGCCCCTAAGCTCCTGATCTA ...@@ -10,8 +10,8 @@ TGCCGGGCAGTCAGGGCATTAGAAATGATTTAGGCTGGTATCAGCAGAAACCAGGGNAAAGCCCCTAAGCTCCTGATCTA
>TRDV2*03 2/4/3 TRAJ48*01 [TRA+D] >TRDV2*03 2/4/3 TRAJ48*01 [TRA+D]
ACTGGTACAGGAAGACCCAAGGTAACACAATGACTTTCATATACCGAGAAAAGGACATCTATGGCCCTGGTTTCAAAGACAATTTCCAAGGTGACATTGATATTGCAAAGAACCTGGCTGTACTTAAGATACTTGCACCATCAGAGAGAGATGAAGGGTCTTACTACTGTGCCTGTGACAGAGACTAACTTTGGAAATGAGAAATTAACCTTTGGGACTGGAACAAGACTCACCATCATACCCAGTAAGTTCTTCATCCTTGGTCAGGAAATCAGCCTGCATAAGATTCTGGGGAA ACTGGTACAGGAAGACCCAAGGTAACACAATGACTTTCATATACCGAGAAAAGGACATCTATGGCCCTGGTTTCAAAGACAATTTCCAAGGTGACATTGATATTGCAAAGAACCTGGCTGTACTTAAGATACTTGCACCATCAGAGAGAGATGAAGGGTCTTACTACTGTGCCTGTGACAGAGACTAACTTTGGAAATGAGAAATTAACCTTTGGGACTGGAACAAGACTCACCATCATACCCAGTAAGTTCTTCATCCTTGGTCAGGAAATCAGCCTGCATAAGATTCTGGGGAA
>TRGV5*01 (5/4/3 TRGJ1*01, 5/4/0 TRGJ1*02) [TRG] >TRGV5*01 (5/4/3 TRGJ2*01, 5/4/0 TRGJ1*02) [TRG]
TTCCGTTCTNCCAACTNCAANGGNNGGTNGTTGGGAATCAGGNACTCAGTNCCAGGNAAAGTATTATACTCATACACCCAGGAGGTGGAGCTGGATATTGATACTACGAAATCTAATTGAAAATGATTCTGGGGTCTATTACTGTGCCACCTGGGCCTTTTATTATAAGAAACTCTTTGGCAGTGGAACAACACTTGTTGTCACAGGTAAGTATCGGAAGAAA TTCCGTTCTNCCAACTNCAANGGNNGGTNGTTGGGAATCAGGNACTCAGTNCCAGGNAAAGTATTATACTCATACACCCAGGAGGTGGAGCTGGATATTGATACTACGAAATCTAATTGAAAATGATTCTGGGGTCTATTACTGTGCCACCTGGGCCTTTTATTATAAGAAACTCTTTGGCAGTGGAACAACACTTGTTGTCACAGGTAAGTATCGGAAGAAA
>TRGV4*02 (4/4/4 TRGJ1*01, 4/4/1 TRGJ1*02, 1/1/1 TRGJ1*02) [TRG] >TRGV4*02 (4/4/1 TRGJ2*01, 1/1/1 TRGJ2*01, 4/4/1 TRGJ1*02, 1/1/1 TRGJ1*02) [TRG]
GGTTTTNTTCGTTGCCNTCCNTTTTTTGNTGGAATCAGGAATCAGCCCAGGGAAAGTATGATACTTACGGAAGCACAAGGTAAGAACTTGAGAATGATACTGCGAAATCTTATTGAAAATGACTCTGGAGTCTATTACTGTGCCACCTGGGAAGGCTATTATAAGAAACTCTTTGGCAGTGGAACAACACTTGTTGTCACAGGTAAGTATCGGAAGATATTCC GGTTTTNTTCGTTGCCNTCCNTTTTTTGNTGGAATCAGGAATCAGCCCAGGGAAAGTATGATACTTACGGAAGCACAAGGTAAGAACTTGAGAATGATACTGCGAAATCTTATTGAAAATGACTCTGGAGTCTATTACTGTGCCACCTGGGAAGGCTATTATAAGAAACTCTTTGGCAGTGGAACAACACTTGTTGTCACAGGTAAGTATCGGAAGATATTCC
\ No newline at end of file
>TRGV1*01, TRGV5*01 0//0 TRGJ1*01 [TRG] >(TRGV1*01, TRGV3*01, TRGV5*01) 0//0 (TRGJ1*01, TRGJ2*01) [TRG]
NNNNNNNNNNNN NNNNNNNNNNNN
tactgtgccacctgggacagg tactgtgccacctgggacagg
gaattattataagaaactctt gaattattataagaaactctt
......
...@@ -80,7 +80,7 @@ GCTGGCAGATTCTGCAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGG ...@@ -80,7 +80,7 @@ GCTGGCAGATTCTGCAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGG
CGGGGTAGTCTCCTGCAGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAGGGATCATCCCTATCTTTGGTACAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACGAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGGGGGGGCTGGAACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGTAAAACTTATCCTTGGAAAGACGTCATCCGTAGTAGTAGTTCAGCCCCCCTGCCGTAATACAGGCCGTGTCTCGATCTCAGCGGCTCACTCCTGGTGGGCTGTGCTTGTGGAATTCTCCCGGTAATCGTGACTTTGCCCTGGAAATTCTATGCCTATTGTTGCTGGACC CGGGGTAGTCTCCTGCAGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAGGGATCATCCCTATCTTTGGTACAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACGAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGGGGGGGCTGGAACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGTAAAACTTATCCTTGGAAAGACGTCATCCGTAGTAGTAGTTCAGCCCCCCTGCCGTAATACAGGCCGTGTCTCGATCTCAGCGGCTCACTCCTGGTGGGCTGTGCTTGTGGAATTCTCCCGGTAATCGTGACTTTGCCCTGGAAATTCTATGCCTATTGTTGCTGGACC
#1428 vh2 #1428 vh2
>(IGHV2-70*04 IGHJ6*02, IGHV2-70D*04 IGHJ6*02) [IGH] >(IGHV2-70*04 IGHJ6*02, IGHV2-70D*04 IGHJ6*02) [IGH]
CCACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGTTGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGTAAAACCACGTCCTTGGCCCGACTCCATACCACACCTAATACCTGGCTGTGTCCACGAGGATCCATGGTTGGGCATTGTAGGACCACTGGTTTTTGGAAGTTCCCTTGAGAAAAGAAAAACAGAATCTTCAAAAAA CCACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGTTGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGTAAAACCACGTCCTTGGCCCGACTCCATACCACACCTAATACCTGGCTGTGTCCACGAGGATCCATGGTTGGGCATTGTAGGACCACTGGTTTTTGGAAGTTCCCTTGAGAAAAGAAAAACAGAATCTTCAAAAAA
#1428 vh3 #1428 vh3
......
>IGHV1-18*01, IGHV7-4-1*02 0//0 IGHD1-1*01 0//0 IGHJ1*01 [IGH] >IGHV 0//0 IGHD1-1*01 0//0 IGHJ1*01 [IGH]
actgtgcgagaga actgtgcgagaga
ggtacaactggaacgac ggtacaactggaacgac
gctgaatacttcc gctgaatacttcc
>IGHV1-18*01 0//0 IGHD3-16*01 0//0 IGHJ4*01 [IGH] >(IGHV1-18*01, IGHV1-18*04) 0//0 IGHD3-16*01 0//0 IGHJ4*01 [IGH]
agcctacatggagctgaggagcctgagatctgacgacacggccgtgtattactgtgcgagaga agcctacatggagctgaggagcctgagatctgacgacacggccgtgtattactgtgcgagaga
gtattatgattacgtttgggggagttatgcttatacc gtattatgattacgtttgggggagttatgcttatacc
actactttgactactggggccaaggaaccctggtcaccgtctcctcag actactttgactactggggccaaggaaccctggtcaccgtctcctcag
# Same sequence, but with only the 20bp start of J # Same sequence, but with only the 20bp start of J
>IGHV1-18*01 0//0 IGHD3-16*01 0//0 IGHJ4*01 [IGH] BUG >(IGHV1-18*01, IGHV1-18*04) 0//0 IGHD3-16*01 0//0 (IGHJ4*01, IGHJ4*02) [IGH] BUG
agcctacatggagctgaggagcctgagatctgacgacacggccgtgtattactgtgcgagaga agcctacatggagctgaggagcctgagatctgacgacacggccgtgtattactgtgcgagaga
gtattatgattacgtttgggggagttatgcttatacc gtattatgattacgtttgggggagttatgcttatacc
actactttgactactggggcc actactttgactactggggcc
# Same sequence, but with only the 15bp start of J # Same sequence, but with only the 15bp start of J
>IGHV1-18*01 0//0 IGHD3-16*01 0//0 IGHJ4*01 [IGH] BUG-LOCUS >(IGHV1-18*01, IGHV1-18*04) 0//0 IGHD3-16*01 0//0 (IGHJ4*01, IGHJ4*02) [IGH] BUG-LOCUS
agcctacatggagctgaggagcctgagatctgacgacacggccgtgtattactgtgcgagaga agcctacatggagctgaggagcctgagatctgacgacacggccgtgtattactgtgcgagaga
gtattatgattacgtttgggggagttatgcttatacc gtattatgattacgtttgggggagttatgcttatacc
actactttgactactg actactttgactactg
\ No newline at end of file
>IGLV1-36*01 0//25 IGLJ1*01
cagtctgtgctgactcagccaccctcggtgtctgaagcccccaggcagagggtcaccatctcctgttctggaagcagctccaacatcggaaataatgctgtaaactggtaccagcagctcccaggaaaggctcccaaactcctcatctattatgatgatctgctgccctcaggggtctctgaccgattctctggctccaagtctggcacctcagcctccctggccatcagtgggctccagtctgaggatgaggctgattattactgtgcagcatgggatgacagcctgaatggtcc
gtcaccgtcctaggagtctgctgtctggggatagcggggagccaggtgtactg
\ No newline at end of file
...@@ -27,7 +27,7 @@ TACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAGGTAAG ...@@ -27,7 +27,7 @@ TACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAGGTAAG
### IGK: VJ, V-KDE, Intron-KDE ### IGK: VJ, V-KDE, Intron-KDE
# 1043-IGK # 1043-IGK
>IGKV1-5*03 9/4/1 IGKJ1*01 [IGK] {CQQYNRLWTF} >IGKV1-5*03 (9/4/1 IGKJ1*01, 9/7/4 IGKJ4*02) [IGK] {CQQYNRLWTF}
CTCCTGCTACTCTGGCTCCCAGGTGCCAAATGTGACATCCAGATGACCCAGTCTCCTTCCACCCTGTCTGCGTCTGTAGGAGACAGAGTCACCATCACCTGCCGGGCCAGTCAGAGTATTAATAACAACTTGGCCTGGTATCAGGAGAAGCCAGGGAAAGCCCCTAAGGTCCTGATCTATAAGGCGTCTAGTTTAGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGAATTCACTCTCACCATCAGCAGCCTGCAGCCTGATGATTTTGCAACCTATTACTGCCAACAATATAATAGACTTTGGACGTTCGGCCAAGGGACCAAGGTGGAAGTCAAACGAACTGTGGCTGCACCATCT CTCCTGCTACTCTGGCTCCCAGGTGCCAAATGTGACATCCAGATGACCCAGTCTCCTTCCACCCTGTCTGCGTCTGTAGGAGACAGAGTCACCATCACCTGCCGGGCCAGTCAGAGTATTAATAACAACTTGGCCTGGTATCAGGAGAAGCCAGGGAAAGCCCCTAAGGTCCTGATCTATAAGGCGTCTAGTTTAGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGAATTCACTCTCACCATCAGCAGCCTGCAGCCTGATGATTTTGCAACCTATTACTGCCAACAATATAATAGACTTTGGACGTTCGGCCAAGGGACCAAGGTGGAAGTCAAACGAACTGTGGCTGCACCATCT
# 0119-lil-IGK+-TRA+D-TRD+-TRG # 0119-lil-IGK+-TRA+D-TRD+-TRG
......
...@@ -14,7 +14,7 @@ ...@@ -14,7 +14,7 @@
"description": "Human T-cell receptor, alpha locus (14q11.2)", "description": "Human T-cell receptor, alpha locus (14q11.2)",
"recombinations": [ { "recombinations": [ {
"5": ["TRAV.fa"], "5": ["TRAV.fa"],
"3": ["TRAJ.fa"] "3": ["TRAJ+down.fa"]
} ], } ],
"parameters": { "parameters": {
"seed": "13s" "seed": "13s"
...@@ -28,7 +28,7 @@ ...@@ -28,7 +28,7 @@
"recombinations": [ { "recombinations": [ {
"5": ["TRBV.fa"], "5": ["TRBV.fa"],
"4": ["TRBD.fa"], "4": ["TRBD.fa"],
"3": ["TRBJ.fa"] "3": ["TRBJ+down.fa"]
} ], } ],
"parameters": { "parameters": {
"seed": "12s" "seed": "12s"
...@@ -41,7 +41,7 @@ ...@@ -41,7 +41,7 @@
"follows": "TRB", "follows": "TRB",
"recombinations": [ { "recombinations": [ {
"5": ["TRBD+up.fa"], "5": ["TRBD+up.fa"],
"3": ["TRBJ.fa"] "3": ["TRBJ+down.fa"]
} ], } ],
"parameters": { "parameters": {
"seed": "12s" "seed": "12s"
...@@ -54,7 +54,7 @@ ...@@ -54,7 +54,7 @@
"description": "Human T-cell receptor, gamma locus (7p14)", "description": "Human T-cell receptor, gamma locus (7p14)",
"recombinations": [ { "recombinations": [ {
"5": ["TRGV.fa"], "5": ["TRGV.fa"],
"3": ["TRGJ.fa"] "3": ["TRGJ+down.fa"]
} ], } ],
"parameters": { "parameters": {
"seed": "10s" "seed": "10s"
...@@ -68,7 +68,7 @@ ...@@ -68,7 +68,7 @@
"recombinations": [ { "recombinations": [ {
"5": ["TRDV.fa"], "5": ["TRDV.fa"],
"4": ["TRDD.fa"], "4": ["TRDD.fa"],
"3": ["TRDJ.fa"] "3": ["TRDJ+down.fa"]
} ], } ],
"parameters": { "parameters": {
"seed": "10s" "seed": "10s"
...@@ -81,10 +81,10 @@ ...@@ -81,10 +81,10 @@
"recombinations": [ { "recombinations": [ {
"5": ["TRDV.fa"], "5": ["TRDV.fa"],
"4": ["TRDD.fa"], "4": ["TRDD.fa"],
"3": ["TRAJ.fa"] "3": ["TRAJ+down.fa"]
}, { }, {
"5": ["TRDD+up.fa"], "5": ["TRDD+up.fa"],
"3": ["TRAJ.fa"] "3": ["TRAJ+down.fa"]
} ], } ],
"parameters": { "parameters": {
"seed": "13s" "seed": "13s"
...@@ -101,7 +101,7 @@ ...@@ -101,7 +101,7 @@
}, { }, {
"5": ["TRDD2+up.fa"], "5": ["TRDD2+up.fa"],
"4": ["TRDD.fa"], "4": ["TRDD.fa"],
"3": ["TRDJ.fa"] "3": ["TRDJ+down.fa"]
}, { }, {
"5": ["TRDD2+up.fa"], "5": ["TRDD2+up.fa"],
"3": ["TRDD3+down.fa"] "3": ["TRDD3+down.fa"]
...@@ -118,7 +118,7 @@ ...@@ -118,7 +118,7 @@
"recombinations": [ { "recombinations": [ {
"5": ["IGHV.fa"], "5": ["IGHV.fa"],
"4": ["IGHD.fa"], "4": ["IGHD.fa"],
"3": ["IGHJ.fa"] "3": ["IGHJ+down.fa"]
} ], } ],
"parameters": { "parameters": {
"seed": "12s" "seed": "12s"
...@@ -131,7 +131,7 @@ ...@@ -131,7 +131,7 @@
"follows": "IGH", "follows": "IGH",
"recombinations": [ { "recombinations": [ {
"5": ["IGHD+up.fa"], "5": ["IGHD+up.fa"],
"3": ["IGHJ.fa"] "3": ["IGHJ+down.fa"]
} ], } ],
"parameters": { "parameters": {
"seed": "12s" "seed": "12s"
...@@ -144,7 +144,7 @@ ...@@ -144,7 +144,7 @@
"description": "Human immunoglobulin, kappa locus (2p11.2)", "description": "Human immunoglobulin, kappa locus (2p11.2)",
"recombinations": [ { "recombinations": [ {
"5": ["IGKV.fa"], "5": ["IGKV.fa"],
"3": ["IGKJ.fa"] "3": ["IGKJ+down.fa"]
} ], } ],
"parameters": { "parameters": {
"seed": "10s" "seed": "10s"
...@@ -170,7 +170,7 @@ ...@@ -170,7 +170,7 @@
"description": "Human immunoglobulin, lambda locus (22q11.2)", "description": "Human immunoglobulin, lambda locus (22q11.2)",
"recombinations": [ { "recombinations": [ {
"5": ["IGLV.fa"], "5": ["IGLV.fa"],
"3": ["IGLJ.fa"] "3": ["IGLJ+down.fa"]
} ], } ],
"parameters": { "parameters": {
"seed": "10s" "seed": "10s"
......
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