Hi David, For a BLAT result filtering, both utilities are fine for simple tasks. pslCDnaFilter is part of the UCSC Source code tree and pslReps is sourced at UCSC from the BLAT package by Kent Informatics. One benefit of using pslCDnaFilter is that you will have more usage options.
Another useful utility for BLAT users is pslToBed. BED format in its most basic version is simply coordinates. Using just this or full BED format with some simple changes should be acceptable input into ShortRead with the user-specified data columns option. Links into the source tree, pre-compiled utilities, and BLAT are on the downloads server: http://hgdownload.cse.ucsc.edu/downloads.html (scroll to the second section titled "Source Downloads") Hopefully we were able to help again, Thank you, Jennifer UCSC Genome Browser Support On 7/20/10 11:08 AM, Drewry, David G.,III (NSTD) wrote: > Jennifer, > > We want to first thank you for your quick response to our previous > questions and the valuable information that you provided us. > > We are trying to complete our analysis on a set of Illumina and 454 data > and are using Blat and Bowtie to map our reads. However, there is little > documentation on the pslCDNa filter and the pslReps filter, which are > used on the blat mapped files. Do you have any specifics on these two > filters and what exactly they are used for (advantages/disadvantages of > one over the other)? > > We also wanted to ask you about whether you are aware of any packages > that support the BLAT format for rna-Seq experiments. Specifically we > have been using other programs such as Genominator and HTSeq which > exploit the ‘ShortRead’ package in R to obtain the counts of exons and > genes. However, these do not seem to support the BLAT format and are > looking for alternatives as BLAT works much better for mapping 454 data. > > Thanks, > > David Drewry > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
