[mira_talk] Re: reducing number of Illumina reads
- From: Egon Ozer <e-ozer@xxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 21 Apr 2011 17:27:56 -0500
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=FastqToCA#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:
>> 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
>
> <bruc.vcf>
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