why merged paired end reads still have strand infomation?
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zwfanwz678 • 0
Last seen 4.5 years ago


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?    



dnaseq rtracklayer paired-end reads • 1.1k views
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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.


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