search

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

Paired-end read support #4

Closed mictadlo closed 8 years ago

mictadlo commented 8 years ago

Hi, HiChip paper ( http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-280 ) describes how they added paired-end support to Sicer:

For paired-end reads, the HiChIP pipeline keeps the first end and extends by the fragment length estimated from mapping positions of the two ends, rather than by the average fragment length of the library. Given the variability of fragment lengths across a complex genome like human genome, the use of actual coordinates of mapped pairs is expected to achieve better resolution in signal visualization. The bed file is then used to generate a bedGraph file by the genomeCoverageBed command from BEDTools.

Best wishes,

Michal

endrebak commented 8 years ago

Thanks. It is definitely on my todo-list (I just had to find PE libs online, since we have no ChIP-seq PE libs ourselves). I will start experimenting with it soon.

endrebak commented 8 years ago

epic now fully supports paired end data, but you need to convert bam them to bedpe first.

bedtools bamtobed -bedpe -i name_sorted_paired_end.bam > file.bedpe