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
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 -
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:
chr10 29334602 29334656 SRR891270.293 255 chr10 61751512 61751575 SRR891270.256 255 chr10 103211892 103212065 SRR891270.153 255
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?