Skip to content

Commit

Permalink
Update ReadMe.md
Browse files Browse the repository at this point in the history
  • Loading branch information
Akmazad committed Sep 25, 2020
1 parent eb91fc1 commit c562dcb
Showing 1 changed file with 2 additions and 2 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -9,11 +9,11 @@ We selected rows that have at least 50% samples have a signal "1" (defined as pe
Next, we need to intersect each peaks with chromosomal bins of fixed-width. Following commands were used to get it done.

```sh
intersectBed -wao -f 0.05 -a hg19_bins_200bp.bed -b mergedPeakHeightMatrix_HumanFC_filtered_signle_label.bed > mergedPeakHeightMatrix_HumanFC_filtered_signle_label.overlaps.bed
intersectBed -wao -f 0.05 -a hg19_bins_200bp.bed -b mergedPeakHeightMatrix_HumanFC_filtered_single_label.bed > mergedPeakHeightMatrix_HumanFC_filtered_single_label.overlaps.bed
```

## Post-processing
- We need to drop few information that aren't relevant (comes from peaks' binIDs after [```intersectBed -wao```](https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html)).
```sh
cut -f1-4,9-10 mergedPeakHeightMatrix_HumanFC_filtered_signle_label.overlaps.bed > mergedPeakHeightMatrix_HumanFC_filtered_signle_label.overlaps.dropped.bed
cut -f1-4,9-10 mergedPeakHeightMatrix_HumanFC_filtered_single_label.overlaps.bed > mergedPeakHeightMatrix_HumanFC_filtered_single_label.overlaps.dropped.bed
```

0 comments on commit c562dcb

Please sign in to comment.