scanBam
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@9977223c
Last seen 4 days ago
Israel

hy, I am working with a bamfile, using the package Rsamtools and the function scanBam, some information that are important for me are return as NA, on galaxy and on IGV i can see the information and I don't undersant why.

srq<-scanBam(bamfile1)

srq[["pos"]]

it is given a list of 220134 entries that are all NA, it is the same for qwidth, mapq, cigar, mpos, isize, rname, strand... what is the problem ? thank you

Rsamtools Rsam • 77 views
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The syntax should be srq[[1]][["pos"]]; your command should return NULL. From the help page ?scanBam, does the command

> fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
> scanBam(fl)[[1]][["pos"]]

work as expected? If not, please report the output of sessionInfo(), mine is

> sessionInfo()
R version 4.2.2 RC (2022-10-27 r83205)
Platform: aarch64-apple-darwin21.6.0 (64-bit)
Running under: macOS Monterey 12.6.2

Matrix products: default
BLAS:   /Users/ma38727/bin/R-4-2-branch/lib/libRblas.dylib
LAPACK: /Users/ma38727/bin/R-4-2-branch/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] Rsamtools_2.14.0     Biostrings_2.66.0    XVector_0.38.0
[4] GenomicRanges_1.50.2 GenomeInfoDb_1.34.4  IRanges_2.32.0
[7] S4Vectors_0.36.1     BiocGenerics_0.44.0

loaded via a namespace (and not attached):
 [1] codetools_0.2-18       crayon_1.5.2           bitops_1.0-7
 [4] zlibbioc_1.45.0        BiocParallel_1.32.5    tools_4.2.2
 [7] RCurl_1.98-1.9         parallel_4.2.2         compiler_4.2.2
[10] GenomeInfoDbData_1.2.9

Also, can you indicate what the position information is likely to be? Is this from a very large genome?

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@james-w-macdonald-5106
Last seen 10 hours ago
United States

scanBam has an argument 'param', which you can set up using ScanBamParam. See ?ScanBamParam for the details.

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