[BioC] filterBam

[Martin Morgan]

On 07/15/2013 11:19 PM, rcaloger wrote:
> Hi,
> I am trying to filter a bam file using a set of coordinates.
> I sorted the bam file using both sortBam or Picard SortSam tools but I always
> get the same error:
>
> filterBam("accepted_hits.sorted.bam", "accepted_hits.tp_exons",
> param=ScanBamParam(which=exons.gr))
>
> Error in
> FUN("/data03/calogero/Documents/singapore/transcripts/semi_synthetic_data_set/for_tm_creation/m1/accepted_hits.tp_exons"[[1L]],
> :
>    failed to build index
>    file:
> /data03/calogero/Documents/singapore/transcripts/semi_synthetic_data_set/for_tm_creation/m1/accepted_hits.tp_exons
>
> In addition: Warning messages:
> 1: In
> FUN("/data03/calogero/Documents/singapore/transcripts/semi_synthetic_data_set/for_tm_creation/m1/accepted_hits.tp_exons"[[1L]],
> :
>    [bam_index_core] the alignment is not sorted (D44TDFP1_1:1:1102:6940:117318):
> 85079683 > 84952092 in 1-th chr
> 2: In
> FUN("/data03/calogero/Documents/singapore/transcripts/semi_synthetic_data_set/for_tm_creation/m1/accepted_hits.tp_exons"[[1L]],
> :
>    [bam_index_build2] fail to index the BAM file.

filterBam tries to place the GRanges into correct order by calling

   bf <- BamFile("accepted_hits.sorted.bam")
   xx <- Rsamtools:::.filterBam_preprocess(bf, param)

after which

   bamWhich(xx)

is supposed to have (a) non-overlapping ranges with (b) seqnames in the same 
order as in the original BAM file and (c) ordered by start position.

I'm supposing that this fails for your exons.gr, and would be happy to 
trouble-shoot if you're willing to share (off-list is fine) the result of

  save(exons.gr, seqlevels(BamFile("accepted_hits.sorted.bam")), file="test.Rda")

Martin

>
>
> Any suggestion how to handle this problem?
> cheers
> Raf
>
>   exons.gr
> GRanges with 3399 ranges and 1 metadata column:
>           seqnames                 ranges strand   | transcriptID
>              <Rle>              <IRanges>  <Rle> |  <character>
>       [1]     chr1   [ 4764598,  4766882]      *   |   uc007aff.2
>       [2]     chr1   [ 7110275,  7110696]      *   |   uc007agb.1
>       [3]     chr1   [ 9858548,  9858769]      *   |   uc007agw.1
>       [4]     chr1   [10029961, 10029968]      *   |   uc007ahk.1
>      ...      ...                    ...    ... ...          ...
>      [3397]     chrX [147525139, 147525147]      *   |   uc012hqq.1
>    [3398]     chrX [148034128, 148034929]      *   |   uc009upe.1
>    [3399]     chrX [156357850, 156359017]      *   |   uc009uss.2
>    ---
>    seqlengths:
>      chr1 chr10 chr11 chr12 chr13 chr14 ...  chr5  chr6  chr7  chr8 chr9  chrX
>        NA    NA    NA    NA    NA    NA ...    NA    NA    NA NA    NA    NA
>
> sessionInfo()
> R version 2.15.3 (2013-03-01)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods base
>
> other attached packages:
> [1] Rsamtools_1.10.2     Biostrings_2.26.3    GenomicRanges_1.10.7
> [4] IRanges_1.16.6       BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
> [1] bitops_1.0-5    parallel_2.15.3 stats4_2.15.3   zlibbioc_1.4.0
>
> -- ----------------------------------------
> Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit MBC Centro di
> Biotecnologie Molecolari Via Nizza 52, Torino 10126 tel. ++39 0116706457 Fax
> ++39 0112366457 Mobile ++39 3333827080 email: raffaele.calogero at unito.it
> raffaele[dot]calogero[at]gmail[dot]com www: http://www.bioinformatica.unito.it
>
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