Over the last few years, RNA-Seq has become an immensely popular technique its own right as an adjunct to microarrays in gene expression studies. The ability to sequence RNA and align it prior to further analyses is a powerful but technically challenging technique. This is largely due to the fact that the powerful sequence aligners are all command-line driven. Sequencher gives you a consistent graphical user interface across its NGS algorithms and access to all the options that you would normally see on the command line.
GSNAP is the algorithm of choice because of its ability to deal with reference genome or transcriptome, splice events, or variants, including multiple mismatches or long indels. It has different alignment modes which allow you to work with data that may contain different SNPs, methylated bases, or RNA-I bases compared to the reference sequence. GSNAP even allows you to sample and align a sub-set of your data to ensure that things went well in the library preparation stages and subsequent sequencing. And if you have any doubts about your data, check its quality with FastQC Reports. Test your reads with eleven separate metrics and produce easy-to-understand reports. You can even use FastQC Reports as a means of tracking the quality over time of the data you are receiving. With the External Data Browser, you can monitor the progress of your alignments – so no more guessing if it’s still running or not.