Does strand information still exist after reads merging?

Question

[Shaway]

hello everyone! I encountered a question and do not know how to tackle with it. I have some reads(using bedtools bamtobed function) like this

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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 -

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and I want to merge these reads and using the output to call peaks by macs2. I take the fisrt number in + strand reads and second number in -strand reads, the output like below:

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chr10   29334602    29334656    SRR891270.293    255

chr10   61751512    61751575    SRR891270.256    255

chr10   103211892   103212065   SRR891270.153    255

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but there are no strand information!

in macs2, the 6 column is needed(For BED format, the 6th column of strand information is required by MACS. And please pay attention that the coordinates in BED format is zero-based and half-open (http://genome.ucsc.edu/FAQ/FAQtracks#tracks1).).

what can I do to solve this problem?

thanks!

Answer 1

[Devon Ryan]

After merging, the concept of strand (actually, it's just orientation) is meaningless. You appear to have a BAM file originally, so just use that as the input to MACS2.

[Shaway]

thanks for you answer.