Question

Can you help me generate a Bsgenome of the fusion genome of a human and HIV-1 virus?

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13273976287 • 0

@a83cdfaa

Last seen 5 months ago

Hong Kong

Hello,

I now need to generate a Bsgenome that is a fusion genome of a person and the HIV-1 virus. I already have the fa files of hg38 and HIV-1 from NCBI. I keep getting errors when running the seed file. I don't know what to use for the genome. In addition, can you help me find out what's wrong with this seed file?

Thanks in advance !

Have a nice day :)

shichen Y

BSgenome.Hsapiens.NCBI.GRCh38 • 454 views

ADD COMMENT • link 6 months ago 13273976287 • 0

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seed:

Package: BSgenome.Hhiv1.NCBI.test
Title: Full genome sequences for HIV-1_hg38 by ysc.
Description: Full genome sequences for HIV-1 and hg38 by ysc.
Version: 1.0.0
organism: Homo sapiens
common_name: Human
genome: hg38
provider: NCBI
release_date: 2023/10/30
organism_biocview: Homo_sapiens
BSgenomeObjname: Hhiv1
seqnames: as.character((read.table("/Users/mac/Desktop/ATAC-genome/HIV-1_hg38.chromName.txt",header=F)$V1)[-c(26:194)])
circ_seqs: "chrM"
seqs_srcdir: /Users/mac/Desktop/ATAC-genome/fa/
seqfiles_suffix: fa
ondisk_seq_format: rda

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seqnames

as.character((read.table("/Users/mac/Desktop/ATAC-genome/HIV-1_hg38.chromName.txt",header=F)$V1)[-c(26:194)])
 [1] "chr1"                        "chr10"                       "chr11"                       "chr12"                      
 [5] "chr13"                       "chr14"                       "chr15"                       "chr16"                      
 [9] "chr17"                       "chr18"                       "chr19"                       "chr2"                       
[13] "chr20"                       "chr21"                       "chr22"                       "chr3"                       
[17] "chr4"                        "chr5"                        "chr6"                        "chr7"                       
[21] "chr8"                        "chr9"                        "chrM"                        "chrX"                       
[25] "chrY"                        "AF033819.3_cds_AAC82593.1_1" "AF033819.3_cds_AAC82598.2_2" "AF033819.3_cds_AAC82594.1_3"
[29] "AF033819.3_cds_AAC82595.1_4" "AF033819.3_cds_AAC82591.1_5" "AF033819.3_cds_AAC82592.1_6" "AF033819.3_cds_AAD20388.1_7"
[33] "AF033819.3_cds_AAC82596.1_8" "AF033819.3_cds_AAC82597.1_9"

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