This package aims to identify annotated and unannotated LINE1 insertion in the genome.
extract_reads
)Reads that are potentially informative for inferring insertion are retrieved, including discordant reads, reads aligning to the sequence of intereset and reads at the region of interest.
cluster_reads
)Reads with MAPQ >= 10 are considered as uniquely mapped and clustered together.
construct_contigs
)For the assembly step, a self-writtern assembly function employing the Overlaps-Layout-Consensus(OLC) method is applied to assemble reads in read cluster into longer contigs.
annotate_contigs
)Contigs are annotated to the regions that they align to. First, contigs are aligned to sequences of interest (e.g a consensus sequence of Hot LINE1). Then, the unaligned parts of the read will be subjected to the next alignment aginst the genome. The first alignment is served as a 'bait' to collect all the sequence of interest, and the second aligment is to locate the insertion site in the genome. In addition, some useful feature, for example, polyA sequence will also be identified and annotated in this step.
infer_transposon
)Under development and will be out soon.
infer_simple_insertion
)extract_reads(bam = "tesing.bam", out_dir = getwd())
reads <- import_files(extracted = "tesing_extracted.txt", anchor_min_mapq = 10)
clusters <- cluster_reads(reads)
clusters <- construct_contigs(clusters) # The most time-consuming sttep;saving the result is recommended
saveRDS(clusters, "test_contigs.rds")
annotation <- annotate_contigs(clusters, insert = "LINE1.fa", genome="hg19.fa")
result <- infer_transposon(annotation) # under development (for LINE1)
extract_reads(bam = "tesing.bam", out_dir = getwd())
reads <- import_files(extracted = "tesing_extracted.txt", anchor_min_mapq = 10)
clusters <- cluster_reads(reads)
clusters <- construct_contigs(clusters)
# Or simply import the result generated for LINE1 insertion
# clusters <- readRDS("test_contigs.rds")
annotation <- annotate_contigs(clusters, insert = "HBV.fa", genome="hg19.fa")
result <- infer_simple_insertion(annotation)
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