[BioC] How to transform a fastq object in granges?

[Valerie Obenchain]

Hi Frederic,

readFastq() produces a ShortReadQ object that holds sequences, quality 
scores and id's from the fastq file. A ShortReadQ cannot be coerced to a 
GRanges because there are no positions (chromosome, start, width, etc.). 
Position is not available because these are unaligned reads.

Valerie


On 07/23/2013 08:01 AM, Frederic Fournier wrote:
> Hello everyone,
>
> Is there a way to create granges object from a fastq obtained from
> readFastq?
>
> Thanks you very much,
>
> Frederic
>
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