README.md

In mskilab/bambi: R to query barcode indices on bam files

bambi

R package for querying 10x WGS and single-cell BAMs

Dependencies

devtools::install_github('mskilab/gUtils')

devtools::install_github('mskilab/bamUtils')

bambi commands

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)

Demo

• Instantiate a bambi object

library(bambi)

> hcc1143_subset = bambi$new(bam_file = "subsetHCC1143_phased_possorted0001.bam", bamdb_path="subsetHCC1143_phased_possorted0001_lmdb")

• Call methods

```{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 ```

mskilab/bambi documentation built on May 14, 2019, 4:04 a.m.