#shape-map

[rnaframework]

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.

[rnaframework]

RNA Framework v2.6 released

This release fixes a few minor bugs, and adds several useful features for the analysis of mutational profiling (MaP) experiments:

- Added support for gzipped FastQ files to rf-map (thanks to Dr. Omar Wagih for feature request, and beta testing) - Introduced rf-map support for quality-based trimming of reads - Introduced new rf-count parameters to enable quality filtering of reads/mappings - Introduced rf-count support for insertions in SHAPE-MaP experiments - Introduced rf-count support for the re-alignment of ambiguously aligned deletions in SHAPE-MaP experiments - Added sampling of Zuker suboptimal structures to rf-fold pseudoknots detection algorithm (increases the searched folding space, and gives more accurate results)

Overall, this version adds several new parameters to rf-count, thus enabling a more accurate handling of mutation/indel events. It appears immediately clear that different parameter combinations produce very different outcomes. Here follows a brief scheme aimed at illustrating the different behaviors with different parameter combinations (dots correspond to sites of assigned mutations):

For additional details please refer to the documentation. Check it out on GitHub!