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
