Dear UCSC Genome Browser developers, We have found that the lengths of mouse chromosomes (mm9) displayed in the Genome Browser are shorter than their actual lengths obtained from the FASTA chromosome sequence data. I used the chromosome data downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/mm9/chromosomes/ to get the actual chromosomal length.
For example, chromosome 3 has a length of 159,599,783 bases in the Genome Browser, however the actual length of chromosome 3 is found to be 162,791,780 bases from the sequence data. This caused a problem when we looked at mapping locations of next-generation sequencing reads which were mapped to the mouse reference genome. We observed our sequencing reads were shifted by ~2 million bases in the Genome Browser. We used mm9 in the Genome Browser and the sequencing reads were also mapping to mm9. Could you please let us know why the chromosomal lengths are different, or are we using Genome Browser in the wrong way? Thanks, ------------------ Wei Shi, Ph.D Bioinformatics Division The Walter and Eliza Hall Institute of Medical Research 1G Royal Parade, Parkville, VIC 3052 Australia ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________ _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
