I'm new to both RNA-seq and bioinformatics itself.
In the project that we're working on we sequenced bacterial RNA from different samples and one of the things we're trying to find from it are deletions and insertions resulting from mistakes in ligation of the RNA.
I have chosen to use bowtie2 for alignment as the argument about which aligner is better seems to be never-ending and also dependant on the situation. But I have seen that people have noted that bowtie2 might prefer a gapped alignment to another non-gapped alignment in some situations.
We had a crazy idea of first using bowtie to map all reads and then filter out all the reads that bowtie did not map(as bowtie doesn't map reads with indels) and maps them with bowtie2. It seems like this way I could calm myself about getting false positives due to alignment.
Is this a bad idea? I haven't seen anyone propose it, so I suppose there's something wrong with it.