R package for querying 10x WGS and single-cell BAMs
devtools::install_github('mskilab/gUtils')
devtools::install_github('mskilab/bamUtils')
Instantiate a bambi object:
Methods:
grab_bx()
grab_bx(barcodes, query=NULL, data.table = FALSE, verbose = FALSE, mc.cores = 1)
grab_cb()
grab_cb(barcodes, query=NULL, data.table = FALSE, verbose = FALSE, mc.cores = 1)
grab_ub()
grab_ub(barcodes, query=NULL, data.table = FALSE, verbose = FALSE, mc.cores = 1)
fetch_by_tag()
fetch_by_tag(tag, tag_queries, query=NULL, data.table = FALSE, verbose = FALSE, mc.cores = 1)
bambi
objectlibrary(bambi)
> hcc1143_subset = bambi$new(bam_file = "subsetHCC1143_phased_possorted0001.bam", bamdb_path="subsetHCC1143_phased_possorted0001_lmdb")
```{r}
hcc1143_subset$grab_bx('CGACGTGTCCTCTAGC-1') GRanges object with 2 ranges and 11 metadata columns: seqnames ranges strand | | [1] chr1 [147975454, 147975580] + | [2] chr1 [147975675, 147975824] - | qname flag mapq cigar [1] ST-K00126:3:H5TL3BBXX:2:2109:25926:37800 99 16 127M [2] ST-K00126:3:H5TL3BBXX:2:2109:25926:37800 147 16 150M rnext pnext tlen [1] = 147975676 371 [2] = 147975455 -371 seq [1] ATGTCTTCTTCCTCATTATCTGGCACTGGTTAGGAAGCACTCATCTCCATGAAGTCATCTTTTGTTAATTCCTCTGGTGTGGTGTGTATTAGCTCTTAAATTCCTCCAAGATCCATATCTTGCAACC [2] ATCTGGACACAAATTGTACTTTTGTCCAGCACGAATTTATTGTTTTGAGTTTCATGGTTTTCTATATCAACTGATGACATCTTGAAAGGTGTAAGCCTTCCAGACTTCCATGATGTTCTCTCTATTGGGTTTCTCTTTTGCAATGTTGAC qual [1] JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJAJFJJJJJJJJJFJJJJJJJJJJFJJJJFFFJJJFJJJJJJAAJFJJJFAFAFFFJAA<7F< [2] A<7FFFJFFFAJJAAAJJF [1] CGACGTGTCCTCTAGC-1 127 [2] CGACGTGTCCTCTAGC-1 150
seqinfo: 1 sequence from an unspecified genome; no seqlengths ```
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