Tao Liu (τν)

@junaruga I guess so, however, the BAMParser uses the same code and I don't see any error message. Quite strange. I may need to do more tests. https://github.com/taoliu/MACS/blob/36492d89877f647375799d93a588cb1a0b6fbab0/MACS2/IO/Parser.pyx#L1048-L1058

@junaruga Yes. Hopefully, it's fixed in the PR #370 :)

@lufuhao It seems there is some problem in your python environment. The error appeared while installing dependencies. Try to install the dependencies by yourself for numpy and cython. Then download...

> However, when I examine the number of peaks with those q-values (or p-values) by filtering the .narrowPeak file, I see many more in my .narrowPeak than the cutoff-analysis claims....

Hi @olechnwin My understanding of "bowtie (aligned concordantly exactly 1 time + aligned concordantly > 1 times)" is that the pair can only be mapped once -- i.e. uniquely mapped...

@ryrl9703 Normally, we don't expect the 'input' has any batch effect or meaningful differences across biological replicates. Therefore, a common suggestion is to simply merge all input/control data together so...

Hi @MariusGheorghe I put a note in MACS2 help: Also please note that the BEDPE only contains three columns, and is NOT the same BEDPE format used by BEDTOOLS. Here...

@emattei Sorry I haven't noticed that @MariusGheorghe had cut the 1, 2 and 6th columns. The difference actually is caused by the filtering criteria used in MACS2. We removed any...

Hi Zoe, the parameter for the shift model won't make a noticeable difference among species. No matter if it is `--nomodel --shoft -100 --extsize 200` or `--nomodel --shift -75 --extsize...

@LunaPatton You have to put `-g THE_GENOME_SIZE` manually. I checked the sheep genome at UCSC genome browser site. Some suggestions: 1. you may need to get rid of a large...