Skip to content

Commit

Permalink
add fusion genome
Browse files Browse the repository at this point in the history
  • Loading branch information
@zhouyiqi91
zhouyiqi91 committed Oct 11, 2023
1 parent 5bc1980 commit 5b4faac
Show file tree
Hide file tree
Showing 5 changed files with 39 additions and 5 deletions.
5 changes: 5 additions & 0 deletions .gitignore
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,5 +3,10 @@ capture_virus/EBV_genome/*
!capture_virus/EBV_genome/mkref.sh
!capture_virus/EBV_genome/EBV_five_genes.gtf

fusion/genome/*
!fusion/genome/mkref.sh
!fusion/genome/BCR_ABL1_PML_RARA_all.fasta
!fusion/genome/BCR_ABL1_PML_RARA_all_pos.txt

tag/fake_match_dir/05.count/fake_match_dir_matrix_10X/genes.tsv
tag/fake_match_dir/05.count/fake_match_dir_matrix_10X/matrix.mtx
10 changes: 5 additions & 5 deletions capture_virus/EBV_genome/EBV_five_genes.gtf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,11 +12,11 @@ EBV EBV_genome gene 35449 36259 . + . gene_id "EBNA2"; transcript_id "EBNA2";
EBV EBV_genome exon 35449 36259 . + . gene_id "EBNA2"; transcript_id "EBNA2"; exon_number "1"; exon_id "EBNA2.1";
EBV EBV_genome CDS 35449 36259 . + 0 gene_id "EBNA2"; transcript_id "EBNA2"; exon_number "1"; exon_id "EBNA2.1";
EBV EBV_genome start_codon 35449 35451 . + 0 gene_id "EBNA2"; transcript_id "EBNA2"; exon_number "1"; exon_id "EBNA2.1";
EBV EBV_genome gene 89895 90044 . + . gene_id "ZEBRA"; transcript_id "ZEBRA";
EBV EBV_genome exon 89895 90044 . + . gene_id "ZEBRA"; transcript_id "ZEBRA"; exon_number "1"; exon_id "ZEBRA.1";
EBV EBV_genome CDS 89895 90041 . + 0 gene_id "ZEBRA"; transcript_id "ZEBRA"; exon_number "1"; exon_id "ZEBRA.1";
EBV EBV_genome start_codon 89895 89897 . + 0 gene_id "ZEBRA"; transcript_id "ZEBRA"; exon_number "1"; exon_id "ZEBRA.1";
EBV EBV_genome stop_codon 90042 90044 . + 0 gene_id "ZEBRA"; transcript_id "ZEBRA"; exon_number "1"; exon_id "ZEBRA.1";
EBV EBV_genome gene 89895 90044 . - . gene_id "ZEBRA"; transcript_id "ZEBRA";
EBV EBV_genome exon 89895 90044 . - . gene_id "ZEBRA"; transcript_id "ZEBRA"; exon_number "1"; exon_id "ZEBRA.1";
EBV EBV_genome CDS 89898 90044 . - 0 gene_id "ZEBRA"; transcript_id "ZEBRA"; exon_number "1"; exon_id "ZEBRA.1";
EBV EBV_genome start_codon 90042 90044 . - 0 gene_id "ZEBRA"; transcript_id "ZEBRA"; exon_number "1"; exon_id "ZEBRA.1";
EBV EBV_genome stop_codon 89895 89897 . - 0 gene_id "ZEBRA"; transcript_id "ZEBRA"; exon_number "1"; exon_id "ZEBRA.1";
EBV EBV_genome gene 95666 95815 . + . gene_id "EBNA1"; transcript_id "EBNA1";
EBV EBV_genome exon 95666 95815 . + . gene_id "EBNA1"; transcript_id "EBNA1"; exon_number "1"; exon_id "EBNA1.1";
EBV EBV_genome CDS 95666 95812 . + 0 gene_id "EBNA1"; transcript_id "EBNA1"; exon_number "1"; exon_id "EBNA1.1";
Expand Down
16 changes: 16 additions & 0 deletions fusion/genome/BCR_ABL1_PML_RARA_all.fasta
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
>BCRe1_ABL1a2
CATAAGCGGCACCGGCACTGCCCGGTTGTCGTGTCCGAGGCCACCATCGTGGGCGTCCGCAAGACCGGGCAGATCTGGCCCAACGATGGCGAGGGCGCCTTCCATGGAGACGCAGAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAG
>BCRe13_ABL1a2
TGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAGAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCA
>BCRe14_ABL1a2
ATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGG
>BCRe19_ABL1a2
CCGAGGCATGGAGGAGGTGGGCATCTACCGCGTGTCCGGTGTGGCCACGGACATCCAGGCACTGAAGGCAGCCTTCGACGTCAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAA
>PML6_RARA3
GATGTCTCCAATACAACGACAGCCCAGAAGAGGAAGTGCAGCCAGACCCAGTGCCCCAGGAAGGTCATCAAGATGGAGTCTGAGGAGGGGAAGGAGGCAAGGTTGGCTCGGAGCTCCCCGGAGCAGCCCAGGCCCAGCACCTCCAAGGCAGTCTCACCACCCCACCTGGATGGACCGCCTAGCCCCAGGAGCCCCGTCATAGGAAGTGAGGTCTTCCTGCCCAACAGCAACCACGTGGCCAGTGGCGCCGGGGAGGCAGCCATTGAGACCCAGAGCAGCAGTTCTGAAGAGATAGTGCCCAGCCCTCCCTCGCCACCCCCTCTACCCCGCATCTACAAGCCTTGCTTTGTCTGTCAGGACAAGTCCTCAGGCTACCACTATGGGGTCAGCGCCTGTGAGGGCTGCAAG
>PML3_RARA3
CTGGTGCAGAGGATGAAGTGCTACGCCTCGGACCAGGAGGTGCTGGACATGCACGGTTTCCTGCGCCAGGCGCTCTGCCGCCTGCGCCAGGAGGAGCCCCAGAGCCTGCAAGCTGCCGTGCGCACCGATGGCTTCGACGAGTTCAAGGTGCGCCTGCAGGACCTCAGCTCTTGCATCACCCAGGGGAAAGCCATTGAGACCCAGAGCAGCAGTTCTGAAGAGATAGTGCCCAGCCCTCCCTCGCCACCCCCTCTACCCCGCATCTACAAGCCTTGCTTTGTCTGTCAGGACAAGTCCTCAGGCTACCACTATGGGGTCAGCGCCTGTGAGGGCTGCAAG
>PML6_BP_RARA3
CCCGAGGAGGCAGAGAGAGTGAAGGCCCAGGTTCAGGCCCTGGGGCTGGCTGAAGCCCAGCCTATGGCTGTGGTACAGTCAGTGCCCGGGGCACACCCCGTGCCAGTGTACGCCTTCTCCATCAAAGGCCCTTCCTATGGAGAGGATGTCTCCAATACAACGACAGCCCAGAAGAGGAAGTGCAGCCAGACCCAGTGCCCCAGGAAGGTCATCAAGATGGAGTCTGAGCCATTGAGACCCAGAGCAGCAGTTCTGAAGAGATAGTGCCCAGCCCTCCCTCGCCACCCCCTCTACCCCGCATCTACAAGCCTTGCTTTGTCTGTCAGGACAAGTCCTCAGGCTACCACTATGGGGTCAGCGCCTGTGAGGGCTGCAAG
>PML4_RARA3
agaggatgaagtgctacgcctcggaccaggaggtgctggacatgcacggtttcctgcgccaggcgctctgccgcctgcgccaggaggagccccagagcctgcaagctgccgtgcgcaccgatggcttcgacgagttcaaggtgcgcctgcaggacctcagctcttgcatcacccaggggaaagatgcagctgtatccaagaaagccagcccagaggctgccagcactcccagggaccctattgacgttgacctgccattgagacccagagcagcagttctgaagagatagtgcccagccctccctcgccaccccctctaccccgcatctacaagccttgctttgtctgtcaggacaagtcctcaggctaccactatggggtcagcgcctgtgagggctgcaagggcttcttccgccgcagcatccagaagaacatggtgtacacgtgtcaccgggacaagaactgcatcatcaacaag
9 changes: 9 additions & 0 deletions fusion/genome/BCR_ABL1_PML_RARA_all_pos.txt
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
tag pos
BCRe1_ABL1a2 115
BCRe13_ABL1a2 78
BCRe14_ABL1a2 75
BCRe19_ABL1a2 83
PML6_RARA3 259
PML3_RARA3 190
PML6_BP_RARA3 228
PML4_RARA3 254
4 changes: 4 additions & 0 deletions fusion/genome/mkref.sh
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
celescope fusion mkref \
--genome_name BCR_ABL1_PML_RARA_all \
--fasta BCR_ABL1_PML_RARA_all.fasta \
--fusion_pos BCR_ABL1_PML_RARA_all_pos.txt\

0 comments on commit 5b4faac

Please sign in to comment.