Hi, I start to learn IGoR software.I use the command as follows:
(1).igor -set_wd $WDPATH -batch foo -read_seqs ./demo/demo.fasta
(2).igor -set_wd $WDPATH -batch foo -species human -chain IGL -align --all -threads 25
(3).igor -set_wd $WDPATH -batch foo -species human -chain IGL -evaluate -output --scenarios 10
(4).igor -set_wd $WDPATH -batch bar -species human -chain IGL -generate 100
and I get the foo_output:
seq_index;scenario_rank;scenario_proba_cond_seq;GeneChoice_V_gene_Undefined_side_prio7_size69;GeneChoice_J_gene_Undefined_side_prio6_size7;Deletion_V_gene_Three_prime_prio5_size21;Deletion_J_gene_Five_prime_prio5_size23;Insertion_VJ_gene_Undefined_side_prio4_size41;DinucMarkov_VJ_gene_Undefined_side_prio3_size16;Mismatches
39959;1;1;(4);(3);(8);(7);(4);(1,3,1,3);(1,2,3,5,7,8,9,11,13,14,15,16,18,19,20,125,156)
38201;1;0.382984;(41);(2);(2);(4);(0);();(0,2,3,4,6,7,8,9,12,14,17,18,19,48,58,67,166)
38201;2;0.245643;(41);(1);(2);(4);(0);();(0,2,3,4,6,7,8,9,12,14,17,18,19,48,58,67,166)
38201;3;0.193471;(41);(2);(2);(5);(1);(3);(0,2,3,4,6,7,8,9,12,14,17,18,19,48,58,67,166)
How could I get everyone sequence clonotype information,such as:
<html xmlns:v="urn:schemas-microsoft-com:vml"
xmlns:o="urn:schemas-microsoft-com:office:office"
xmlns:x="urn:schemas-microsoft-com:office:excel"
xmlns="http://www.w3.org/TR/REC-html40">
Hi, I start to learn IGoR software.I use the command as follows: (1).igor -set_wd $WDPATH -batch foo -read_seqs ./demo/demo.fasta (2).igor -set_wd $WDPATH -batch foo -species human -chain IGL -align --all -threads 25 (3).igor -set_wd $WDPATH -batch foo -species human -chain IGL -evaluate -output --scenarios 10 (4).igor -set_wd $WDPATH -batch bar -species human -chain IGL -generate 100 and I get the foo_output: seq_index;scenario_rank;scenario_proba_cond_seq;GeneChoice_V_gene_Undefined_side_prio7_size69;GeneChoice_J_gene_Undefined_side_prio6_size7;Deletion_V_gene_Three_prime_prio5_size21;Deletion_J_gene_Five_prime_prio5_size23;Insertion_VJ_gene_Undefined_side_prio4_size41;DinucMarkov_VJ_gene_Undefined_side_prio3_size16;Mismatches 39959;1;1;(4);(3);(8);(7);(4);(1,3,1,3);(1,2,3,5,7,8,9,11,13,14,15,16,18,19,20,125,156) 38201;1;0.382984;(41);(2);(2);(4);(0);();(0,2,3,4,6,7,8,9,12,14,17,18,19,48,58,67,166) 38201;2;0.245643;(41);(1);(2);(4);(0);();(0,2,3,4,6,7,8,9,12,14,17,18,19,48,58,67,166) 38201;3;0.193471;(41);(2);(2);(5);(1);(3);(0,2,3,4,6,7,8,9,12,14,17,18,19,48,58,67,166)
How could I get everyone sequence clonotype information,such as: <html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">
clonotype identifier | representative query sequence name | count | frequency (%) | CDR3 nucleotide sequence | CDR3 amino acid sequence | productive status | chain type | V gene | D gene | J gene -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- 1a | number:1_length:188_4051 | 7 | 0.0241 | CAGTCCTATGACAGCAGCCTGAGTGGTGCGGTG | QSYDSSLSGAV | No | VL | IGLV1-40*01,IGLV1-40*02 | N/A | IGLJ3*02