Hi Michael, The psl file from BLAT is available on our downloads server here: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/all_est.txt.gz
And the EST fasta file from here: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/est.fa.gz (note that this contains ALL of the ESTs for hg18, including those that did not align) You will need to strip the bin column from all_est.txt (it's just a field we use to speed up display in the Genome Browser). One of our engineers mentioned that you will probably want to use the scripts shared here: http://generic-model-organism-system-database.450254.n5.nabble.com/Getting-sequences-into-a-BAM-file-td454848.html Also, chromInfo.txt.gz might be helpful as a source of header info when converting SAM to BAM. That file is located here: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/chromInfo.txt.gz If you have further questions, please feel free to write back to [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 11/22/10 05:52, Michael Morley wrote: > Hi, > > > I'm wondering if there is a file(s) of the BLAT alignments of the human > ESTs to HG18. The hope I have is to be able to convert EST alignments to > BAM files. > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
