[Bioc-sig-seq] large BAM files and large BED files

Martin Morgan mtmorgan at fhcrc.org
Mon Sep 19 20:31:11 CEST 2011

On 09/19/2011 11:26 AM, Rene Paradis wrote:
> Thanks Martin and Michael for your constructive advices,
> I used the ScanBamParam object to successfully load a part of the Chr1
> from a Bam file via ScanBam. Honestly I do not know what are the
> differences between readGappedAlignments, readBamGappedAlignment and
> ScanBam. The last two of them can take a  ScanBamParam object.

scanBam returns a list-of-lists, it's the most flexible but least 

readGappedAlignments is meant to be a 'front end' to read 
GappedAlignments from several different sources, and 
readBamGappedAlignments is meant to be one of those sources; usually the 
'user' would readGappedAlignments.

> But I wished I could select the seqname in GRanges to retrieve all the
> chr1 (as an example) data from the Bam file. It seems I must select a
> range. So I put a value that goes beyond the range of the chr1 because I
> do not know that range, and I got an<<INTEGER () can only be applied to
> a 'integer', not a special>>. There must be something I missed that
> could help me doing that.

see ?scanBamHeader, e.g.,

 >  fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
 > scanBamHeader(fl)[[1]]$targets
seq1 seq2
1575 1584


> ultimately, I want to launch a PICS analysis that requires a
> segReadsList object.
> Overall I definitely progressed by your help, thank you.
> Rene
> On Fri, 2011-09-16 at 14:29 -0700, Martin Morgan wrote:
>> On 09/16/2011 02:11 PM, Michael Lawrence wrote:
>>> It sounds like you're trying to use BED as an alternative to BAM? Probably
>>> not a good idea, especially at this scale. Why are you aiming for a
>>> GenomeData? A GappedAlignments might be more appropriate. See
>>> GenomicRanges::readGappedAlignments() for bringing a BAM into a
>>> GappedAlignments.
>> Hi Rene
>> the 'which' argument to readGappedAlignments (it'll become 'param' with
>> the next release, and be a ScanBamParam object) allows you to select
>> regions to process, e.g., chromosome-at-a-time, to help with file size.
>> Martin
>>> This page might help:
>>> http://bioconductor.org/help/workflows/high-throughput-sequencing/#sequencing-resources
>>> But it could really be improved.
>>> Michael
>>> On Fri, Sep 16, 2011 at 1:44 PM, Rene Paradis<rene.paradis at genome.ulaval.ca
>>>> wrote:
>>>> Hello,
>>>> I am experiencing a problem regarding the load in memory of bed files of
>>>> 30 GB. my function read.table unleash the error : Error in unique(x) :
>>>> length xxxxxx is too large for hashing.
>>>> this is generated by the function MKsetup of the unique.c file. Even by
>>>> increasing by 10 000x the value, the error persists. I believe the
>>>> function pushes more data in ram, but I am not sure this is the good way
>>>> to focus on.
>>>> Ultimately, I would like to produce a GenomeData object from either a
>>>> BAM file or a bed file.
>>>> has someone ever worked with very very big BAM files (about 30 GB)
>>>> thanks
>>>> Rene paradis
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