Question: why merged paired end reads still have strand infomation?
gravatar for zwfanwz678
2.3 years ago by
zwfanwz6780 wrote:


I using package rtracklayer to processing some paired end reads.

using export function, I can convert my data to bed format, but there is a question confused me.

I using bedtools bamtobed function to convert bam file to bed file, the output are as follows:

chr10 29334602 29334652 SRR891270.293/2 255 +

chr10 29334606 29334656 SRR891270.293/1 255 -

chr10 61751512 61751562 SRR891270.256/2 255 +

chr10 61751525 61751575 SRR891270.256/1 255 -

chr10 103211892 103211942 SRR891270.153/2 255 +

chr10 103212015 103212065 SRR891270.153/1 255 -

then , I want using MACS2 to call peaks, so I have to merge these reads and the output I think should be like this:

chr10 29334602 29334656 SRR891270.293 255

chr10 61751512 61751575 SRR891270.256 255

chr10 103211892 103212065 SRR891270.153 255

no strand infomation exist because of merge.

but when I using export function of rtracklayer, the output are

chr10 29334602 29334656 SRR891270.293 0 -

chr10 61751512 61751575 SRR891270.256 0 -

chr10 103211892 103212065 SRR891270.153 0 -

the 5th cloumn is not important, but why the strand infomation still exist?

from what I learned, the paired end principle  is like 


--['+':50bp]-->                                            <--['-':50bp]--

when you merge the 2 reads, it means you get the total reads from its start(the small number) to its end(the large number), why strand info still exist?

Is the package "rtracklayer" wrong or I miss some thing during the merge?    



ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by zwfanwz6780

Please tell us how you are doing the merging. rtracklayer does not do any merging. If you give it strand information, it will output it.

ADD REPLYlink written 2.3 years ago by Michael Lawrence11k
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