losing %reads aligned with Bowtie paired end analysis
Hello all,
I've got paired-end chIP-Seq library data sets (72 bases forward and reverse each, 20 million reads each) from Illumina GA2 runs that I've aligned with Bowtie, chIP against H3K4me1. When combining/catting the forward and reverse reads together and aligning as a single fastq file, I get 97% read alignment. On the other hand, when I align the forward and reverse tags as a true paired analysis, I get 65% of reads aligned. The signal/noise ratio of peaks is the same with either analysis. My fragment size is 125 bp (w/o adapters), and the maximum allowed distance between retained forward and reverse mates is 250bp (the default maximum allowed insert size for Bowtie alignment).
Has anyone got any thoughts on why I am losing so many reads aligned running a paired end analysis versus just combining the forward and reverse reads and aligning that as a single file?
Thanks sincerely for your help!
All the best,
Batool
I've got paired-end chIP-Seq library data sets (72 bases forward and reverse each, 20 million reads each) from Illumina GA2 runs that I've aligned with Bowtie, chIP against H3K4me1. When combining/catting the forward and reverse reads together and aligning as a single fastq file, I get 97% read alignment. On the other hand, when I align the forward and reverse tags as a true paired analysis, I get 65% of reads aligned. The signal/noise ratio of peaks is the same with either analysis. My fragment size is 125 bp (w/o adapters), and the maximum allowed distance between retained forward and reverse mates is 250bp (the default maximum allowed insert size for Bowtie alignment).
Has anyone got any thoughts on why I am losing so many reads aligned running a paired end analysis versus just combining the forward and reverse reads and aligning that as a single file?
Thanks sincerely for your help!
All the best,
Batool