Question: comparing the results of two mapping methods and extract part of them
gravatar for meishengxiao86
5.6 years ago by
meishengxiao8630 wrote:

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!

rna-seq • 1.4k views
ADD COMMENTlink modified 5.6 years ago • written 5.6 years ago by meishengxiao8630

So you wanna know which contig from the tools each read maps to?

ADD REPLYlink written 5.6 years ago by RamRS27k

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. 

ADD REPLYlink written 5.6 years ago by meishengxiao8630
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