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biocore-ntnu / epic

(DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER
http://bioepic.readthedocs.io
MIT License
31 stars 6 forks source link

are read ids necessary in SE mode? #85

Closed avilella closed 5 years ago

avilella commented 5 years ago

In trying to lower the memory requirements of epic, I would like to know if the read ids of the 'bedtools bamtobed' step are necessary in SE mode (i.e. not bedpe)? Would converting the read ids into an incrementing number in column 4 make the running of EPIC less memory hungry?

endrebak commented 5 years ago

Those ids are thrown away as soon as possible (before the data is read into memory even). So it would not affect the memory usage.