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Aaron Quinlan arq5x

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View bedtools_cheatsheet.md

Bedtools Cheatsheet

General:

Tools Description
flank Create new intervals from the flanks of existing intervals.
slop Adjust the size of intervals.
shift Adjust the position of intervals.
subtract Remove intervals based on overlaps b/w two files.
@brentp
brentp / tss.sh
Created Jul 17, 2012
bed file of transcription start-sites (TSS)
View tss.sh
UPSTREAM=400
INSTREAM=100
ORG=hg18
mysql --user genome --host genome-mysql.cse.ucsc.edu -NAD $ORG -e \
"select chrom, txStart, txEnd, X.geneSymbol, strand from knownGene as K, kgXref as X WHERE txStart != txEnd AND X.kgID = K.name" \
| awk -v ups=$UPSTREAM -v ins=$INSTREAM 'BEGIN{OFS=FS="\t"}
$5 == "-" { print $1,$3-ins,$3+ups,$4 }
$5 == "+" { print $1,$2-ins,$2+ups,$4 }' \
| sort -k1,1 -k2,2n \