I improved the mapping of our RNAi reagents (BKN/HD2 and HFA libraries) and wanted to provide you with this data. As you pointed out during your last E-Mail, the gene locations and chromosomal locations of RNAi reagents reported by NEXT-RNAi do not match in every case. This is not a bug, but NEXT-RNAi uses the mappings of potential siRNAs generated from the long dsRNA to define the primary RNAi target. In cases where no gene is annotated for the chromosomal target region, the dsRNA might still have short overlaps to other genes. NEXT-RNAi reports them as 'best targets', although they are not overlapping with the chromosomal target region.
However, as you pointed out, this might be confusing. I now re-calculated the mapping in a simple 2-step approach (based on FlyBase r5.41):
- I first mapped the RNAi reagent (using primer sequences) on the Drosophila genome using isPcr (in silico PCR from UCSC)
- I then used these mappings to define the gene target (using gene mappings from the FlyBase gff file)
For your report, I excluded all RNAi reagents that do have multiple chromosomal locations, target multiple gene (e.g. overlapping gene models) or target no gene at all. I generated a file in the format you requested:
reagentID<tab>chromosomal_location<tab>FBgnID
The file HD2_Mapping_r5.41.tab contains mappings for the BKN/HD2 library, the file HFA_Mapping_r5.41.tab for the HFA library.
Would it be possible for you to replace the data you have by this new data? If you have questions or need further data (e.g. the primer sequences) please let me know.