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Hi all,
This is probably a rather basic question but here it goes. Up until recently I have been doing RNA-seq using single-ended sequence reads. When using bedtools intersect, each read will intersect with a gene once and represent 1 hit to the gene. Now, I am starting to use a stranded paired-end illumina RNA-seq data. With this protocol, I essentially have two reads, the pairs, that came from the same molecule. So when I now use bedtools intersect, will bedtools take into account the paired-reads and treat them as a single event, or will get two lines of output, 1 for each of the two pairs?
Basically, I just want to know if bedtools is aware that there are two reads for each molecule that was sequence and takes this into account. This could be important when determining coverage, as it would double count each molecule
This is probably a rather basic question but here it goes. Up until recently I have been doing RNA-seq using single-ended sequence reads. When using bedtools intersect, each read will intersect with a gene once and represent 1 hit to the gene. Now, I am starting to use a stranded paired-end illumina RNA-seq data. With this protocol, I essentially have two reads, the pairs, that came from the same molecule. So when I now use bedtools intersect, will bedtools take into account the paired-reads and treat them as a single event, or will get two lines of output, 1 for each of the two pairs?
Basically, I just want to know if bedtools is aware that there are two reads for each molecule that was sequence and takes this into account. This could be important when determining coverage, as it would double count each molecule