Description

This track shows mappings of all near full length (>6000 nt) L1PA5->4 instances in Gibbon to the corresponding Repeat Browser consensus.

Display Conventions and Configuration

The track is a coverage track of all elements found in the labeled genome. Drops in coverage indicate lack of alignment (e.g. a deletion).

Use this track to see if deletions or insertions correspond to factor binding.

Methods

#get the L1PA from the rmsk file, sort it, merge it [sometimes L1PA not full merged!!!] but don't merge two giant things, filter on full length

cat legend.txt | while read i; do grep -P "\t${1}\t" ${i}_RepeatMasker.bed | bedtools sort | bedtools merge -s | awk '$3-$2>6000' > ${i}_${1}_full.bed; done

#get sequence

cat legend.txt | while read i; do twoBitToFa -bed=${i}_${1}_full.bed -bedPos https://hgdownload.soe.ucsc.edu/gbdb/${i}.2bit ${i}_${1}_full.fa; done

#blat

cat legend.txt | while read i; do blat RepeatBrowserConsensus/${1}.fa ${i}_${1}_full.fa ${i}_${1}_full.psl; done

#make coverage track

cat legend.txt |while read i; do psl2cov.sh ${i}_${1}_full.psl ~/public_html/RepeatBrowserHub/hg38reps/hg38reps.sizes bw/${i}_${1}_full.bw; done

References