Hi, I mapped my RNAseq data with two different methods, tophat and bowtie2. For the result of tophat I used the full length reads(150nt) for mapping and only the unique alignment was selected. For the result of bowtie2, I only used the first 50nt in local model when mapping and permit multiple alignments in output file. Finally, I would like to use the result from tophat to determine the origin of the reads and at the same time by using the alignment information to find out the corresponding unique alignment from multiple hits in bowtie2 output file. But I do not know how to do that. Does anyone could give me some suggestions? I am learning python, if the code or idea is based on python would be better. Any suggestions and comments are welcome!!! Thanks a lot in advance!
So you wanna know which contig from the tools each read maps to?
For tophat, I only keep the unique alignment in the sam file and each read will have one specific origin, however, for alignments in bowite output file, there will be multiple alignments for each read. What I want to do is to pick out the one specific alignment from multiple hits of each read by comparing the location information with that of the unique alignment of the same read in tophat output.