I have paired end exome sequence data for 50 human genes only. I have mapped the exome data to hg19 assembly using bowtie2 with default parameters.
bowtie2 --end-to-end -x /path/to/human/genome -q -1 input1.fastq -2 input2.fastq -S output.sam
after the alignment, I used Picard samsort tool to sort the file and convert to bam file.
When I view the alignment, we found that there are some regions where only reverse reads are mapped and there were no forward reads.
The question is:
In theory, Bowtie should only consider forward and reverse reads simultaneously for the mapping. However, because of some quality issue, only reverse reads are aligned. Is this true?
Is this, alignment issue or trimming issue?
Is this a bigger problem for interpretation of mutations (SNPs)
which parameter/flag should I use to make a better alignment.
Thanks in advance