Hi all,
I have some pair-end RNA-Seq datasets, 50bp*2 with 200bp inserts. Now I have mapped them with Tophat, and my question is, how should I manipulate the mapped reads in bam file to distinguish signal on the opposite strand from the paired reads that mapped on the opposite strand? For example, a gene on the + strand is detected with expression, then it will have paired reads mapped on the - strand about 200bp downstream from the reads that mapped on the + strand, then how do I distinguish these reads from a real gene on the - strand and is also expressed? Is there any specialized tool to do this? Or any genome browser can visualize PE reads?
I have some pair-end RNA-Seq datasets, 50bp*2 with 200bp inserts. Now I have mapped them with Tophat, and my question is, how should I manipulate the mapped reads in bam file to distinguish signal on the opposite strand from the paired reads that mapped on the opposite strand? For example, a gene on the + strand is detected with expression, then it will have paired reads mapped on the - strand about 200bp downstream from the reads that mapped on the + strand, then how do I distinguish these reads from a real gene on the - strand and is also expressed? Is there any specialized tool to do this? Or any genome browser can visualize PE reads?