Issues with ChipSeq mapping

[Chipper]

My guess is you didn't trim your reads and are reading into the adaptor. Try bwa mem if you have 100 or 125 bp reads.

[priya]

Hi,
I have ChipSeq data, and I mapped the reads with bowtie aligner using mm10 as reference genome.
Out of 16M reads processed, only 3M reads are uniquely mapped and 11M reads failed to align and 2M reads are not uniquely mapped.
It looks soo strange that most of the reads are failed to align, I also tried to collect the unaligned sequences and run blast for several species on random 5000 sequences, the highest percentage of unaligned sequences were coming from Mouse.

I couldnt find explaination, if there is not much species contamination in the chipseq samples, then why the reads are not aligning to the mouse genome.

Also, choice of aligner instead of bowtie, if I use BWA will it make any difference..
What could be the considerations for this problem??


Here is the bowtie log

# reads processed: 16561198
# reads with at least one reported alignment: 3860809 (23.31%)
# reads that failed to align: 10781729 (65.10%)
# reads with alignments suppressed due to -m: 1918660 (11.59%)
Reported 3860809 alignments to 1 output stream(s)