Exporting formatted alignments and clonotypes
MiXCR is able to export alignments and clonotypes as pretty formatted human-readable text for manual analysis. This is useful both to inspect alignments and to facilitate optimization of analysis parameters and library preparation protocol.
Raw alignments
mixcr exportAlignmentsPretty
[--top]
[--gene]
[--limit-before <n>]
[--limit <n>]
[--chains <chains>]
[--skip <n>]
[--cdr3-equals <seq>]
[--feature <gene_feature>]
[--read-contains <seq>]
[--filter <s>]
[--descriptions]
[--read-ids <id>]...
[--clone-ids <id>]...
[--force-overwrite]
[--no-warnings]
[--verbose]
[--help]
alignments.(vdjca|clna) [output.txt]
.vdjca file. alignments.(vdjca|clna)- Path to input file with alignments.
[output.txt]- Path where to write export. Will write to output if omitted.
-t, --top- Output only top hits
-a, --gene- Output full gene sequence
-b, --limit-before <n>- Limit number of alignments before filtering
-n, --limit <n>- Limit number of filtered alignments; no more than N alignments will be outputted
-s, --skip <n>- Number of output alignments to skip
-c, --chains <chains>- Filter export to a specific protein chain gene (e.g. TRA or IGH). Default: ALL
-e, --cdr3-equals <seq>- Output only alignments where CDR3 exactly equals to given sequence
-g, --feature <gene_feature>- Output only alignments which contain a corresponding gene feature
-r, --read-contains <seq>- Output only alignments where target read contains a given substring
--filter <s>- Custom filter
-d, --descriptions- Print read descriptions
-i, --read-ids <id>- List of read ids to export
--clone-ids <id>- List of clone ids to export
-f, --force-overwrite- Force overwrite of output file(s).
-nw, --no-warnings- Suppress all warning messages.
--verbose- Verbose messages.
-h, --help- Show this help message and exit.
Example:
> mixcr exportAlignmentsPretty --skip 1000 --limit 10 input.vdjca
Pretty alignments have the following structure:
>>> Read id: 1
5'UTR><L1
Quality 88888888888888888888888887888888888888888888888888888888888888888888888887888878
Target0 0 AAGGCCTTTCCACTTGGTGATCAGCACTGAGCACAGAGGACTCACCATGGAGTTGGGGCTGAGCTGGGTTTTCCTTGTTG 79
IGHV3-7*00 54 aaggcctttccacttggtgatcagcactgagcacagaggactcaccatggaAttggggctgagctgggttttccttgttg 133
L1><L2 L2><FR1
Quality 88888888887888888888888888888889989989989889999997999999989999999999999999999899
Target0 80 CTATTTTAGAAGGTGTCCAGTGTGAGGTGAAGTTGGTGGAGTCTGGGGGAGGCCTGGTCCAGCCTGGGGGGTCCCTGAGA 159
IGHV3-7*00 134 ctattttagaaggtgtccagtgtgaggtgCagCtggtggagtctgggggaggcTtggtccagcctggggggtccctgaga 213
FR1><CDR1 CDR1><FR2
Quality 999999999999999999999999999999999999999999999 9999999999999999999999999999999999
Target0 160 CTCTCCTGTGAAGCCTCCGGATTCACCTTTAGTAGTTATTGGATG-GCATGGGTCCGCCAGGGTCCAGGGCAGGGGCTGG 238
IGHV3-7*00 214 ctctcctgtgCagcctcTggattcacctttagtagCtattggatgAgc-tgggtccgccaggCtccagggAaggggctgg 292
FR2><CDR2 CDR2><FR3
Quality 99999999999999999999999999999999999799999999999999999999999999998999899898999999
Target0 239 AATGGGTGGGCAACATAAGGCCGGATGGAAGTGAGAGTTGGTACTTGGAGTCTGTGATGGGGCGATTCATGATATCTAGA 318
IGHV3-7*00 293 aGtgggtggCcaacataaAgcAAgatggaagtgagaAAtACtaTGtggaCtctgtgaAgggCcgattcaCCatCtcCaga 372
FR3><CDR3
Quality 99899899999999988989999889979988888888878878788888888878888888778788888888878888
Target0 319 GACAACGCCAAGAAGTCACTTTATCTGCAAATGGACAGCCTGAGAGTCGAGGACACGGCCGTCTATTATTGTGCGACTTC 398
IGHV3-7*00 373 gacaacgccaagaaCtcactGtatctgcaaatgAacagcctgagagCcgaggacacggcTgtGtattaCtgtgcga 448
IGHD3-10*00 12 ttc 14
CDR3><FR4
Quality 88888788888888888888888787788777887787777877777877787787877878788788777767778788
Target0 399 GGAGGAGCCGGAGGACTACTGGGGCCAGGGAGCCCTGGTCACCGTCTCCTCGGCTTCCACCAAGGGCCCATCGGTCTTCC 478
IGHD3-10*00 15 gg-ggag 20
IGHJ4*00 8 gactactggggccagggaAccctggtcaccgtctcctc 45
IGHG4*00 0 cttccaccaagggcccatcggtcttcc 26
IGHG3*00 0 cttccaccaagggcccatcggtcttcc 26
IGHG2*00 0 cCtccaccaagggcccatcggtcttcc 26
IGHG1*00 0 cCtccaccaagggcccatcggtcttcc 26
IGHGP*00 194 AgcCtccaccaagggcccatcggtcttcc 222
Quality 87370
Target0 479 CCTTG 483
IGHG4*00 27 ccCtg 31
IGHG3*00 27 ccCtg 31
IGHG2*00 27 ccCtg 31
IGHG1*00 27 ccCtg 31
IGHGP*00 223 ccCtg 227
Usage of the --verbose option will produce alignments in a slightly different format:
>>> Read id: 12343 <--- Index of analysed read in input file >>> Target sequences (input sequences): Sequence0: <--- Read 1 from paired-end read Contains features: CDR1, VRegionTrimmed, L2, L, Intron, VLIntronL, FR1, Exon1, <--- Gene features VExon2Trimmed found in read 1 0 TCTTGGGGGATTCGGTGATCAGCACTGAACACAGAGGACTCACCATGGAGTTTGGGCTGAACTGGGTTTTCCTCGTTGCT 79 <--- Sequyence & quality FGGEGGGGGDG8F78CFC6CEFF<,CFG9EED,6,CFCC<EEGFG,CE:CCAFFGGC87CEF?A?FBC@FGGFG>B,FC9 of read 1 80 CTATTAAGAGGTGTCCAGTGTCAGGTGCAGCTGGTGGAGTCTGGGGGTGGCGTGTTCCAGCCTGGGGGGTCCGTGAGACT 159 F9,A,95AFE,B?,E,C,9AC<FGA<EE5??,A,A<:=:E,=B8C7+++8,++@+,885=D7:@8E+:5*1**11**++< 160 CTCCTGTGCAGCGTCGGGATGCACATCATGGAGCTATGGCCAGCCCTGGGTACGCCAGGCTACAGGCCACGGGCTGGAGG 239 <++*++0++2A:ECE5EC5**2@C+:++++++22*2:+29+*2***25/79*0299))*/)*0*0*.75)7:)1)1/))) 240 GGGTGCGTGGTAGATGGGAA 259 )9:.)))*1)12***-/).) Sequence1: <--- Read 2 from paired-end read Contains features: JCDR3Part, DCDR3Part, DJJunction, CDR2, JRegionTrimmed, CDR3, VDJunction, VJJunction, VCDR3Part, ShortCDR3, FR4, FR3 0 CGAGGCAAGAGGCTGGTGTGGGTGGCGGTTATATGGTATGGTGGAAGTAATAAACACTATGCAGACCCCGTGAAGGGCCG 79 **0*0**)2**/**5D7<15*9<5:1+*0:GF:=C>6A52++*:2+++FF>>3<++++++302**:**/<+**;:/**2+ 80 ATTCACCATCGCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAAGAGCCTGAGAGCCGAGGACACGGCTTTGT 159 +++<0***C:2+9GGFB?,5,4,+,2F<>FC=*,,C:>,=,@,,;3<@=,3,,<3,CF?=**<>@,?3,<<:3,CC,E,@ 160 ATTACTGTGCGAGAGGTCAACAGGGTGACTATGTCTACGGTAGGGACGTCGGGGGCCAAGGGACCACGGTCACCGTCTCC 239 ,@;FCF@+F@FGGF9FD,F>>+B:=,,=><GFCGGCFEGFF?+=B+7EF>+FFA,8F<E:,5+GDFFE,@F?,,7GGDFE 240 TCAGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCTCTGCGTTGATACCACTGGCAGCTC 300 C,FGGGEFCCGEEGGCFCC:8FGEGGGE@DFB-GFGGGGF@GFGFE<,GFCCFCAGC@CCC >>> Gene features that can be extracted from this (paired-)read: <--- For paired-end reads JCDR3Part, CDR1, VRegionTrimmed, L2, DCDR3Part, VDJTranscriptWithout5UTR, Exon2, L, some gene features DJJunction, Intron, FR2, CDR2, VDJRegion, JRegionTrimmed, CDR3, VDJunction, VJJunction, can be extracted by VLIntronL, FR1, VCDR3Part, ShortCDR3, Exon1, FR4, VExon2Trimmed, FR3 merging sequence information >>> Alignments with V gene: IGHV3-33*00 (total score = 1638.0) <--- Alignment of both reads with IGHV3-33 Alignment of Sequence0 (score = 899.0): <--- Alignment of IGHV3-33 with read 1 from paired-end read 65 ATTCGGTGATCAGCACTGAACACAGAGGACTCACCATGGAGTTTGGGCTGAGCTGGGTTTTCCTCGTTGCTCTTTTAAGA 144 <--- Germline ||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||| |||||| 9 ATTCGGTGATCAGCACTGAACACAGAGGACTCACCATGGAGTTTGGGCTGAACTGGGTTTTCCTCGTTGCTCTATTAAGA 88 <--- Read DG8F78CFC6CEFF<,CFG9EED,6,CFCC<EEGFG,CE:CCAFFGGC87CEF?A?FBC@FGGFG>B,FC9F9,A,95AF <--- Quality score 145 GGTGTCCAGTGTCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGC 224 |||||||||||||||||||||||||||||||||||||| |||||| ||||||||||| ||||| |||||||||||||||| 89 GGTGTCCAGTGTCAGGTGCAGCTGGTGGAGTCTGGGGGTGGCGTGTTCCAGCCTGGGGGGTCCGTGAGACTCTCCTGTGC 168 E,B?,E,C,9AC<FGA<EE5??,A,A<:=:E,=B8C7+++8,++@+,885=D7:@8E+:5*1**11**++<<++*++0++ 225 AGCGTCTGGATTCACCTTCA-GTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTG 300 |||||| |||| || | ||| | ||||||||| || |||||| ||||||||| ||||| | ||||||||| ||||| 169 AGCGTCGGGATGCA-CATCATGGAGCTATGGCCAGCCCTGGGTACGCCAGGCTACAGGCCACGGGCTGGAGGGGGTG 244 2A:ECE5EC5**2@ C+:++++++22*2:+29+*2***25/79*0299))*/)*0*0*.75)7:)1)1/))))9:.) Alignment of Sequence1 (score = 739.0): <--- Alignment of IGHV3-33 with read 2 from paired-end read 279 AGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGAT 358 ||||||| |||||| ||||||||| ||||||||||||| ||||||||||||| ||||||||||| ||||||||||||||| 2 AGGCAAGAGGCTGGTGTGGGTGGCGGTTATATGGTATGGTGGAAGTAATAAACACTATGCAGACCCCGTGAAGGGCCGAT 81 0*0**)2**/**5D7<15*9<5:1+*0:GF:=C>6A52++*:2+++FF>>3<++++++302**:**/<+**;:/**2+++ 359 TCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTAT 438 |||||||| |||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||| ||||| 82 TCACCATCGCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAAGAGCCTGAGAGCCGAGGACACGGCTTTGTAT 161 +<0***C:2+9GGFB?,5,4,+,2F<>FC=*,,C:>,=,@,,;3<@=,3,,<3,CF?=**<>@,?3,<<:3,CC,E,@,@ 439 TACTGTGCGAGAG 451 ||||||||||||| 162 TACTGTGCGAGAG 174 ;FCF@+F@FGGF9 IGHV3-30*00 (total score = 1582.0) <--- Alternative hit for V gene Alignment of Sequence0 (score = 885.0): 65 ATTCGGTGATCAGCACTGAACACAGAGGACTCACCATGGAGTTTGGGCTGAGCTGGGTTTTCCTCGTTGCTCTTTTAAGA 144 ||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||| |||||| 9 ATTCGGTGATCAGCACTGAACACAGAGGACTCACCATGGAGTTTGGGCTGAACTGGGTTTTCCTCGTTGCTCTATTAAGA 88 DG8F78CFC6CEFF<,CFG9EED,6,CFCC<EEGFG,CE:CCAFFGGC87CEF?A?FBC@FGGFG>B,FC9F9,A,95AF 145 GGTGTCCAGTGTCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGC 224 |||||||||||||||||||||||||||||||||||||| |||||| ||||||||||| ||||| |||||||||||||||| 89 GGTGTCCAGTGTCAGGTGCAGCTGGTGGAGTCTGGGGGTGGCGTGTTCCAGCCTGGGGGGTCCGTGAGACTCTCCTGTGC 168 E,B?,E,C,9AC<FGA<EE5??,A,A<:=:E,=B8C7+++8,++@+,885=D7:@8E+:5*1**11**++<<++*++0++ 225 AGCCTCTGGATTCACCTTCA-GTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTG 300 ||| || |||| || | ||| | ||||||||| || |||||| ||||||||| ||||| | ||||||||| ||||| 169 AGCGTCGGGATGCA-CATCATGGAGCTATGGCCAGCCCTGGGTACGCCAGGCTACAGGCCACGGGCTGGAGGGGGTG 244 2A:ECE5EC5**2@ C+:++++++22*2:+29+*2***25/79*0299))*/)*0*0*.75)7:)1)1/))))9:.) Alignment of Sequence1 (score = 697.0): 279 AGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGAT 358 ||||||| |||||| ||||||||| ||||||| |||| ||||||||||||| ||||||||||| ||||||||||||||| 2 AGGCAAGAGGCTGGTGTGGGTGGCGGTTATATGGTATGGTGGAAGTAATAAACACTATGCAGACCCCGTGAAGGGCCGAT 81 0*0**)2**/**5D7<15*9<5:1+*0:GF:=C>6A52++*:2+++FF>>3<++++++302**:**/<+**;:/**2+++ 359 TCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTAT 438 |||||||| |||||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||||||| ||||| 82 TCACCATCGCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAAGAGCCTGAGAGCCGAGGACACGGCTTTGTAT 161 +<0***C:2+9GGFB?,5,4,+,2F<>FC=*,,C:>,=,@,,;3<@=,3,,<3,CF?=**<>@,?3,<<:3,CC,E,@,@ 439 TACTGTGCGAGAG 451 ||||||||||||| 162 TACTGTGCGAGAG 174 ;FCF@+F@FGGF9 >>> Alignments with D gene: IGHD4-17*00 (total score = 40.0) Alignment of Sequence1 (score = 40.0): 7 GGTGACTA 14 |||||||| 183 GGTGACTA 190 :=,,=><G IGHD4-23*00 (total score = 36.0) Alignment of Sequence1 (score = 36.0): 0 TGACTACGGT 9 || ||||||| 191 TGTCTACGGT 200 FCGGCFEGFF IGHD2-21*00 (total score = 35.0) Alignment of Sequence1 (score = 35.0): 13 GGTGACT 19 ||||||| 183 GGTGACT 189 :=,,=>< >>> Alignments with J gene: IGHJ6*00 (total score = 172.0) Alignment of Sequence1 (score = 172.0): 22 GGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCA 61 ||||||| ||||| |||||||||||||||||||||||||| 203 GGACGTCGGGGGCCAAGGGACCACGGTCACCGTCTCCTCA 242 =B+7EF>+FFA,8F<E:,5+GDFFE,@F?,,7GGDFEC,F >>> Alignments with C gene: No hits.
Clonotypes
mixcr exportClonesPretty
[--limitBefore <n>]
[--limit <n>]
[--skip <n>]
[--clone-ids <id>]...
[--chains <chains>]
[--cdr3-equals <seq>]
[--clonal-sequence-contains <seq>]
[--force-overwrite]
[--no-warnings]
[--verbose]
[--help]
clones.(clns|clna) [output.txt]
.clnx files. Especially useful after assembleContigs to manually check how contig clonotypes are covered. clones.(clns|clna)- Path to input file with clones
[output.txt]- Path where to write export. Will write to output if omitted.
-b, --limitBefore <n>- Limit number of alignments before filtering
-n, --limit <n>- Limit number of filtered alignments; no more than N alignments will be outputted
-s, --skip <n>- Number of output alignments to skip
-i, --clone-ids <id>- List of clone ids to export
-c, --chains <chains>- Filter export to a specific protein chain gene (e.g. TRA or IGH). Default: ALL
-e, --cdr3-equals <seq>- Only output clones where CDR3 (not whole clonal sequence) exactly equals to given sequence
-r, --clonal-sequence-contains <seq>- Only output clones where target clonal sequence contains sub-sequence.
-f, --force-overwrite- Force overwrite of output file(s).
-nw, --no-warnings- Suppress all warning messages.
--verbose- Verbose messages.
-h, --help- Show this help message and exit.