Question: Error in parsing BAM file using readAlligned
gravatar for kspata
21 months ago by
kspata70 wrote:


I was trying to find number of reads within a specific target region. To perform this I found the post on Biostar A: How To Extract Reads From Bam That Overlap With Specific Regions?

I installed the necessary packages into an R Studion session and performed the following command.

reads <- readAligned("Sample.sorted.bam", type = "BAM")

I am getting following error

Error: UserArgumentMismatch arugment 'type' had value 'BAM' allowable values: 'SolexaExport' 'SolexaAlign' 'SolexaPrealign' 'SolexaRealign' 'SolexaResult' 'MAQMap' 'MAQMapShort' 'MAQMapview' 'Bowtie' 'SOAP'

If I change the command to:

reads <- readAligned("Sample.sorted.bam", type = "Bowtie")

I am getting this error:

Error: Input/Output 'readAligned' failed to parse files dirPath: 'Sample.sorted.bam' pattern: '' type: 'Bowtie' error: incorrect number of fields (1) 749827-1.sorted.bam:1

My R session Info:

R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] rtracklayer_1.42.1          ShortRead_1.40.0            GenomicAlignments_1.18.0   
 [4] SummarizedExperiment_1.12.0 DelayedArray_0.8.0          matrixStats_0.54.0         
 [7] Biobase_2.42.0              Rsamtools_1.34.0            GenomicRanges_1.34.0       
[10] GenomeInfoDb_1.18.1         Biostrings_2.50.1           XVector_0.22.0             
[13] IRanges_2.16.0              S4Vectors_0.20.1            BiocParallel_1.16.2        
[16] BiocGenerics_0.28.0        

loaded via a namespace (and not attached):
 [1] zlibbioc_1.28.0        lattice_0.20-35        hwriter_1.3.2          tools_3.5.1           
 [5] grid_3.5.1             latticeExtra_0.6-28    Matrix_1.2-14          GenomeInfoDbData_1.2.0
 [9] RColorBrewer_1.1-2     BiocManager_1.30.4     bitops_1.0-6           RCurl_1.95-4.11       
[13] compiler_3.5.1         XML_3.98-1.16

How can I resolve this error and parse the BAM file?

alignment R gene • 551 views
ADD COMMENTlink modified 21 months ago by swbarnes28.6k • written 21 months ago by kspata70
gravatar for swbarnes2
21 months ago by
United States
swbarnes28.6k wrote:

Solexa? SOAP? That's an 8 year old solution. I recommend finding something a little more up to date, like BEDTools.

ADD COMMENTlink written 21 months ago by swbarnes28.6k

Thank you for replying. I tried using samtools command

samtools view Sample.bam "ref:6000-11000" > region.bam

My original Sample.bam has 3264461 number of mapped reads and for the region.bam I got 3203443 number of reads.

I think this command also includes the reads which overlap outside the given range as well. I want number of reads which are within this region for example, reads with mapping start at 6000 and end at 11000.

ADD REPLYlink written 21 months ago by kspata70

BEDTools can be that specific.

ADD REPLYlink written 21 months ago by swbarnes28.6k
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