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UCSC liftover tool

UCSC liftover

Issue: separate peaks map to same coordinates after liftover

  • When using the tool to liftover regions from hg19 to hg38, separate peaks in specific regions of hg19 map to overlapping coordinates after liftover.
  • This is because some contigs were not carried forward from hg19 to hg38, due to problems with the hg19 assembly that were resolved in hg38
  • All lifted over peaks with overlapping coordinates should be removed from analysis because the peaks were called on an uncertain region in the old genome assembly
  • Issues like this likely apply to all genome updates, not only human
  • The same issue also applies with Ensembl assembly converter


Remove any peaks with overlapping coordinates after liftover before using the lifted over peak file:


module load bedtools


# Sort the lifted over peakfile for use with bedtools
sort -k1,1 -k2,2n ${EXTL}wong_fig3c_peaks_GRCh38.bed > ${EXTL}peaks.tmp && mv ${EXTL}peaks.tmp ${EXTL}wong_fig3c_peaks_GRCh38.bed

# Bedtools merge count rows contributing to merged peaks (overlapping peaks will have count > 1)
bedtools merge -i ${EXTL}wong_fig3c_peaks_GRCh38.bed -c 1 -o count > ${EXTL}counted.bed

# Get non-overlapping peaks
awk '/\t1$/{print}' ${EXTL}counted.bed > ${EXTL}filtered.bed

# Intersect original file with non-overlapping peaks and output overlapping peaks
bedtools intersect -wa -a ${EXTL}wong_fig3c_peaks_GRCh38.bed -b ${EXTL}filtered.bed > ${EXTL}wong_fig3c_peaks_GRCh38_correct_liftover.bed
bedtools intersect -v -a ${EXTL}wong_fig3c_peaks_GRCh38.bed -b ${EXTL}filtered.bed > ${EXTL}wong_fig3c_peaks_GRCh38_overlapping.bed