How to transform a fastq object in granges?
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@frederic-fournier-5663
Last seen 8.4 years ago
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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@valerie-obenchain-4275
Last seen 13 months ago
United States
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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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