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

[Martin Morgan]

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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