Hi All
I am new on this Forum and I have an issue that I hope you can help me to solve.
I have strand specific paired-end RNA sequencing and I would like to extract the strand information of reads that fall in a particular genomic region (from bam file)
Obviously I have to consider the first in pair to determine the strand orientation (because in paired-end one of reads is always on the opposite strand).
For example, I would like to know if reads falling in chr1:122592431-123294331 are located in plus or minus strand (in bam file).
How would you do it?Any suggestion?
Thank you
I am new on this Forum and I have an issue that I hope you can help me to solve.
I have strand specific paired-end RNA sequencing and I would like to extract the strand information of reads that fall in a particular genomic region (from bam file)
Obviously I have to consider the first in pair to determine the strand orientation (because in paired-end one of reads is always on the opposite strand).
For example, I would like to know if reads falling in chr1:122592431-123294331 are located in plus or minus strand (in bam file).
How would you do it?Any suggestion?
Thank you
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