[Bioc-sig-seq] Calculating insert size for paired-end /mate pair samples

[Tyler Backman]

I forgot to mention- this is for use with ShortRead.

Sincerely,
Tyler William H Backman
Bioinformatics Analyst
Institute for Integrative Genome Biology (IIGB)
Department of Botany and Plant Sciences
E-mail: tyler.backman at ucr.edu
1207E Genomics Building
University of California
Riverside, CA 92521

On Jan 20, 2010, at 10:13 AM, Tyler Backman wrote:

> Hello Abhi,
> 
> Here is an example for calculating insert size of GA reads via a bowtie alignment:
> 
> # align with bowtie
> system("bowtie -q reference.fasta -1 "pair1filtered.fastq" -2 "pair2filtered.fastq" -n 3 -e 160 -p 5 -I 0 -X 500 --fr > alignment.bowtie")
> # import alignment
> alignedReads <- readAligned("./", pattern="alignment.bowtie", type="Bowtie")
> # calculate insert sizes
> distance <- position(alignedReads[seq(2,length(alignedReads),by=2)]) - position(alignedReads[seq(1,length(alignedReads),by=2)]) + width(alignedReads)[1]
> # look at stats
> median(distance)
> sd(distance)
> 
> Sincerely,
> Tyler William H Backman
> Bioinformatics Analyst
> Institute for Integrative Genome Biology (IIGB)
> Department of Botany and Plant Sciences
> E-mail: tyler.backman at ucr.edu
> 1207E Genomics Building
> University of California
> Riverside, CA 92521
> 
> On Jan 20, 2010, at 9:52 AM, Pratap, Abhishek wrote:
> 
>> Hi All
>> 
>> Recently it has been quiet here. I hope you all had a good start to 2010.
>> 
>> I wanted to know if there is already a method in ShortRead or some other package to calculate the insert size for pair end or mate pair data from GA and plot it on a graph. I guess the latter part is trivial.
>> 
>> Thanks,
>> -Abhi
>> 
>> 
>> 	[[alternative HTML version deleted]]
>> 
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