Thanks Tyler for a quick reply. I see with few manipulations we can get to the insert size. Although this isn't bad but it will be nice to include direct function in ShortRead to infer insert size.
Cheers, -Abhi -----Original Message----- From: Tyler Backman [mailto:[email protected]] Sent: Wednesday, January 20, 2010 1:17 PM To: Tyler Backman Cc: Pratap, Abhishek; [email protected] Subject: Re: [Bioc-sig-seq] Calculating insert size for paired-end /mate pair samples 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: [email protected] 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: [email protected] > 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]] >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
