I finally got to reading the paper on RNase E. The amount of bioinformatics work on the paper is very impressive! I didn’t understand a few things though and it would be nice if one could discuss them.
Regarding our PAR-CLIP paper, we did initially get the Hafner lab (who invented PAR-CLIP) to analyze the data, but they found few peaks. On the other hand, when I analyzed the data myself, I found T>C diagnostic changes in many genes, and I later showed through experimentation that several of these changes are biologically relevant. So, I am not sure whether analyzing the data through peak identification is the best way to go.
However, I did also try to use Paralyzer on my data but got errors. I am not sure whether the data was properly formatted for Paralyzer. Do you have any suggestions?
Also, as I mentioned earlier, I would ideally like to use only reads that contain T>C mutations for motif identification and remove background reads. So if it is possible using Galaxy tools, that would be great. I also tried to use MEME on unfiltered reads but got an error. Perhaps I don’t know how to format the Bam file for MEME. Any advice would be appreciated.
Finally, it is possible that for future projects we may need someone who has experience with bioinformatics. Would you be open to collaboration or know anyone who might be?