I found that there is a "collapse" tool under FASTA manipulation, which will significantly shorten mapping time with bowtie with small RNA reads that tend to have many reads of exact length and sequence after clipping adaptors. The tool generates new names for each unique sequence read with a number indicating the number of times (or occurrences) the unique sequence has appeared in the data. The question is, after mapping with Bowtie, how can I regain this "occurrence" information when displaying in Genome Browser? The current setting will only show one mapped read for each unique sequence, no matter how many times this unique sequence has occurred. Should I write a custom code to expand the resulting sam file based on the occurrences?
All runs were executed on the galaxy main server. Any suggestion is appreciated. Jun