Hi Thong, You don't need to convert the coordinate in BED file. The BED file includes a "strand" field which indicates whether it is "+" or "-". You can find more information about the BED file format here:
http://genome.ucsc.edu/FAQ/FAQformat.html#format1 Also, this previous answered mailing question may help you in understanding genomic coordinates better. https://lists.soe.ucsc.edu/pipermail/genome/2009-June/019383.html Hope this helps you. If you have further questions, please don't hesitate in contacting the mailing list again. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "NGUYEN Trung Thong" <[email protected]> To: [email protected] Sent: Saturday, August 7, 2010 10:19:38 AM GMT -08:00 US/Canada Pacific Subject: [Genome] Reverse strand coordinate Dear friends, I would like to check if a line in BED file belongs to a specific genomic region (e.g. start = chr1 100; end= chr1 1000). If the line is in reverse strand, do I need to convert its coordinate present in BED file by the following formula before checking? start = (chromSize - lineEnd) + 1 end = chromSize - (lineStart - 1) Thanks a lot, Thong -- NGUYEN Trung Thong School of Mathematics, Statistics and Applied Mathematics NUI Galway, Ireland _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
