RNA Framework v2.6.6 (minor) released
This release fixes a bug in rf-fold causing the software to get stuck when trying to generate graphical reports for transcripts with only 0/NaN reactivity values (thanks to Dr. Uciel Pablo Chorostecki for reporting this bug).
Moreover, this version introduces a new feature in the rf-count utility. Now, it is possible to specify transcript regions that must be excluded from RT-stops/mutations/coverage counting. This feature is particularly useful when dealing with targeted mutational profiling-based (MaP) structure probing experiments (see below).
In the above example, targeted SHAPE-MaP analysis of a long transcript has been performed by using 9 tiling primer pairs. PCR products from either odd primer pairs or even primer pairs have been pooled ans sequenced independently, then mapped to the reference transcript. At this stage, rf-count can be used to count the number of mutation events per base. A mask file, containing either the sequence or the 1-based coordinates of the primer annealing regions, is provided along with the analyzed BAM file. The two generated RC files generated can be then combined using the merge tool of the rf-rctools utility. The resulting merged RC file can be then normalized by the rf-norm software, yielding the final reactivity profile for the full transcript.
For additional details, please refer to the documentation.
