Dear Martin,
many thanks for the information.

I got the point:
in exons.gr:
seqlevels(exons.gr)
  [1] "chr1"  "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" 
"chr17"
[10] "chr18" "chr19" "chr2"  "chr3"  "chr4"  "chr5"  "chr6" "chr7"  "chr8"
[19] "chr9"  "chrX"

seqlevels(BamFile("accepted_hits.sorted.bam")
  [1] "chr1"  "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" 
"chr17"
[10] "chr18" "chr19" "chr2"  "chr3"  "chr4"  "chr5"  "chr6" "chr7"  "chr8"
[19] "chr9"  "chrM"  "chrX"  "chrY"

  "chrM" is missing in exons.gr

There is any simple way to add to exons.gr also the chrM?
you can get the test.Rda at :
https://mail.unito.it/mailftp/uplister/get_file.php?file=ZmlsZXMvRjEvNDAvZDBjMGExMTk0OTkyYWM3YzY4Nzg0MTFlYjc1My80MzA0ZWU0MzA1OGMzYTBhMmQ1NWZjMWZjNDM4M2M5ZQ==
Many thanks !
Raf

the file I used to generate exon.gr was ordered by chr and then by start 
position

On 7/16/13 1:25 PM, Martin Morgan wrote:
> 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@unito.it
>> raffaele[dot]calogero[at]gmail[dot]com www: 
>> http://www.bioinformatica.unito.it
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
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>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>


-- 

----------------------------------------
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@unito.it
        raffaele[dot]calogero[at]gmail[dot]com
www:   http://www.bioinformatica.unito.it


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