[mira_talk] reducing number of Illumina reads
- From: "Goldman, Thomas" <Thomas.Goldman@xxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 21 Apr 2011 16:27:24 -0500
Hello all,
I have a 24GB RHEL5 machine on which I was able to do a de novo assembly
of 454 paired-end and fragment reads (~1.5 million reads). I also have
about 6 million 36bp Illumina reads.
I would like to:
1) Map the Illumina reads to the 454 backbone
2) Include the Illumina reads with the 454 reads for a de novo
assembly
But I believe I don't have enough memory to handle all the Illumina
reads. I think my VM could handle maybe 20% of the Illumina reads. What
is the best way to reduce the Illumina reads used for the mapping and/or
the de novo assemblies? Would it be to just randomly pick 20% of the
reads out of the fastq file? Is there a tool out there I could use for
this?
Thanks,
Tom
Other related posts:
