Hi, guys, I am thinking the way to utilize those unmapped reads.
When I mapped PE100 data using TopHat, some reads were threw out as unmapped reads.
When I looked into these unmapped reads, though a lot are garbage or mis-matched reads, I found some of them contained information. Thus, I am thinking to utilize these unmapped data. I gave TopHat a specific GTF and asked the data mapped to this GTF with -G option.
However, I found that though with a good mapping rate (>80%), only a small percentage of reads are properly aligned (~20%). I think that's because the unmapped data of paired-end reads ( left vs right) are not synchronized.
Can I synchronize the unmapped left and right reads with some recommended tools?
Or do you think if this idea worth time spending?
Thanks,
When I mapped PE100 data using TopHat, some reads were threw out as unmapped reads.
When I looked into these unmapped reads, though a lot are garbage or mis-matched reads, I found some of them contained information. Thus, I am thinking to utilize these unmapped data. I gave TopHat a specific GTF and asked the data mapped to this GTF with -G option.
However, I found that though with a good mapping rate (>80%), only a small percentage of reads are properly aligned (~20%). I think that's because the unmapped data of paired-end reads ( left vs right) are not synchronized.
Can I synchronize the unmapped left and right reads with some recommended tools?
Or do you think if this idea worth time spending?
Thanks,
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