Question: Rsamtools: error with quickBamFlagSummary
0
gravatar for bsmith030465
12 months ago by
bsmith030465110
United States
bsmith030465110 wrote:

Hi,

I was trying to determine if my bam file was single or pair ended. However, when I try to use Rsamtools, I get an error:

> quickBamFlagSummary(file="/Users/bsmith/Documents/run_s1_Aligned_Reads.bam")
Error: identical(length(N_1seg_rec_per_uqname) + length(N_mseg_rec_per_uqname),  .... is not TRUE

> traceback()

9: stop(msg, call. = FALSE, domain = NA)
8: stopifnot(identical(length(N_1seg_rec_per_uqname) + length(N_mseg_rec_per_uqname), 
   length(N_rec_per_uqname)))
7: quickBamFlagSummary(res0, param = param, main.groups.only = main.groups.only)
6: quickBamFlagSummary(res0, param = param, main.groups.only = main.groups.only)
5: quickBamFlagSummary(file, param = param, main.groups.only = main.groups.only)
4: quickBamFlagSummary(file, param = param, main.groups.only = main.groups.only)
3: .local(file, ..., param = param, main.groups.only = main.groups.only)
2: quickBamFlagSummary(file = "/Users/bsmith/Documents/run_s1_Aligned_Reads.bam")
1: quickBamFlagSummary(file = "/Users/bsmith/Documents/run_s1_Aligned_Reads.bam")

Is there something I need to do differently? Its a RNA seq data, if that helps any...

thanks!

rna-seq rsamtools • 260 views
ADD COMMENTlink written 12 months ago by bsmith030465110
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