[mira_talk] Re: reducing number of Illumina reads
- From: "Goldman, Thomas" <Thomas.Goldman@xxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 21 Apr 2011 17:34:14 -0500
Thanks Egon. Yes, simple enough. Just thought I would see if there was
something better to do than just random removal of reads.
-Tom
From: mira_talk-bounce@xxxxxxxxxxxxx
[mailto:mira_talk-bounce@xxxxxxxxxxxxx] On Behalf Of Egon Ozer
Sent: Thursday, April 21, 2011 3:28 PM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: reducing number of Illumina reads
fastqSample distributed with the wgs-assembler package can subset your
fastq files for you. I haven't checked to see if it picks random or
series (i.e. every 3rd or every 4th, etc) of reads.
There's a little blurb about it at the bottom of this page:
http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Fast
qToCA#fastqSample
Otherwise it wouldn't be too tough to write a quick perl script to
output every fifth read from your data set to another file.
- E
On Apr 21, 2011, at 5:08 PM, Robert Bruccoleri wrote:
However, there is a problem with taking this approach -- you could
significantly change the statistics for the determination of repetitive
regions and cause misassemblies as a result.
Mira will generate coverage equivalent reads which can help in this
situation.
--Bob
ALLO (Alfredo Lopez De Leon) wrote:
You can try to collapse your reads with the FASTX toolkit this will
leave you with a set made of unique reads.
This method will preserve the sequence coverage and remove the
redundancy.
http://hannonlab.cshl.edu/fastx_toolkit/
AlLo
From: mira_talk-bounce@xxxxxxxxxxxxx
[mailto:mira_talk-bounce@xxxxxxxxxxxxx] On Behalf Of Goldman, Thomas
Sent: Thursday, April 21, 2011 2:27 PM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] reducing number of Illumina reads
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:
Map the Illumina reads to the 454 backbone
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
<bruc.vcf>
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