Incorporate results from GEO into jBrowse

Today maybe very specific hint, but some of you may find it useful. I was looking for a way of incorporating the data from GEO in jBrowse. First, I’ve generated BED file out of results in proprietary format, then I have converted this to bedGraph and bigWig following the hint from BioStars. is available through github.

# convert GEO to BED
zcat GSE53693_allinfo_final_ORFs.txt.gz | cut -f3,4,9 | ../../ref/DANRE.gtf > GSE53693.bed

# BED 2 BedGraph
sort -k1,1 -k2,2n GSE53693.bed | bedtools merge -scores max | awk ‘{printf "%st%dt%dt%2.3fn" , $1,$2,$3,$4}’ >
# using bedtools2
#sort -k1,1 -k2,2n GSE53693.bed | bedtools merge -c 5 -o max | awk ‘{printf "%st%dt%dt%2.3fn" , $1,$2,$3,$4}’ >

# bedGraph 2 BigWig
bedGraphToBigWig ../../ref/DANRE.fa.fai


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