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aryeelab / hichipper

A preprocessing and QC pipeline for HiChIP data
MIT License
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the difference between *.interaction.txt.gz and *.filt.intra.loop_counts.bedpe #53

Open WenChangYu opened 6 years ago

WenChangYu commented 6 years ago

Hi,

Hichipper documentation said .interaction.txt.gz and .filt.intra.loop_counts.bedpe are identical except in presentation, so I think their number of rows are the same. But in my hichipper output files, the rows number are different, .interaction.txt.gz has more rows than .filt.intra.loop_counts.bedpe dose.

Is there something wrong in using the hichipper?

Thanks in advance

caleblareau commented 6 years ago

Can you send me the number of lines in each output file?