Question: Does strand information still exist after reads merging?
1
gravatar for Shaway
2.2 years ago by
Shaway10
Shaway10 wrote:

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?

thanks!

chip-seq • 656 views
ADD COMMENTlink modified 2.2 years ago by Devon Ryan92k • written 2.2 years ago by Shaway10
1
gravatar for Devon Ryan
2.2 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

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.

ADD COMMENTlink written 2.2 years ago by Devon Ryan92k

thanks for you answer.

ADD REPLYlink written 2.2 years ago by Shaway10
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