Hi kuldeep5534, thank you for your message! I have modified the according paired-end sequencing data import function to avoid adding length of the reads: regions[plus, "stop"] = regions[plus, "start"] + regions[plus, "isize"] + extend regions[!plus, "start"] = regions[!plus, "stop"] + regions[!plus,"isize" ] - extend This should soon be available in dev v. 1.17.4. All the best, Lukas > On 21 Mar 2015, at 12:32, kuldeep5534 [bioc] <noreply@bioconductor.org> wrote: > > Activity on a post you are following on support.bioconductor.org <https: support.bioconductor.org=""/> > User kuldeep5534 <https: support.bioconductor.org="" u="" 7497=""/> wrote Question: MEDIPS : Populating fragments from Paired End reads <https: support.bioconductor.org="" p="" 65901=""/>: > > > > Hi Lukas, > > I have a question about MeDIP R script. > > MEDIPS/R/MEDIPS.readRegionsFile.R > > > regions = data.frame(chr=as.character(as.vector(regions$rname)), start=as.numeric(as.vector(regions$pos)), stop=as.numeric(as.vector(regions$pos)+as.vector(regions$qwidth)-1), strand=as.character(as.vector(regions$strand)), isize=as.numeric(as.vector(regions$isize)), stringsAsFactors=F) > > plus=regions$strand=="+" > > regions[plus, "stop"] = regions[plus, "stop"] + regions[plus, "isize"] + extend <------ line 153 > > regions[!plus, "start"] = regions[!plus, "start"] + regions[!plus,"isize" ] - extend <------ line 154 > > regions[, "stop"]=regions[, "stop"]+shift > > regions[, "start"]=regions[, "start"]+shift > > > > Let's take 'extend' to be zero, then template/fragment should be from start of first mate to end of second mate. > > Insertion length is defined as distance between start of first mate and end of second mate. So it should have been > > > regions[plus, "stop"] = regions[plus, "start"] + regions[plus, "isize"] > > | | | > > | | | > > end of second mate start of first mate insertion size > > > Your implementation is adding extra length which is equal to read length of first mate. > > And I have same opinion for line 154 as well. > > > Have it been done intentionally? > > Please! Correct me if my understanding is wrong. > > > Image link given below will help to understand if still the question is not clear. > > https://cloud.githubusercontent.com/assets/1637382/6764850/66028a8e-cfeb-11e4-8cbc-2605d664acb3.jpg <https: cloud.githubusercontent.com="" assets="" 1637382="" 6764850="" 66028a8e-cfeb-11e4-8cbc-2605d664acb3.jpg=""> > Thanks for any help. > > > You may reply via email or visit MEDIPS : Populating fragments from Paired End reads >