Hi everyone,
First time poster here
I'm trying to align some Illumina paired reads (88bp) to the HIV1 reference (NC_001802.1, ~10k bp) using Bowtie2. However, somehow I found that these reads only align to the first half of the reference (refer to attachment).
This seems to be consistent across aligners (Bowtie2 & BWA), so I'm suspecting that it might be a characteristic of HIV. Has anyone come across any similar findings or suggestions?
Thanks!
First time poster here
I'm trying to align some Illumina paired reads (88bp) to the HIV1 reference (NC_001802.1, ~10k bp) using Bowtie2. However, somehow I found that these reads only align to the first half of the reference (refer to attachment).
This seems to be consistent across aligners (Bowtie2 & BWA), so I'm suspecting that it might be a characteristic of HIV. Has anyone come across any similar findings or suggestions?
Thanks!
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