always reads on plus strand more than on minus strand

[tujchl]

HI:
I use quest to analysis my chip-seq data, after collapsing reads I found on every chromosome, reads on plus strand are more than on minus strand (example are below), Does it indicate some problem? (I filter out redundant reads before quest)
thank you in advance

sorting hits

-------------------------
contig: chr1

+ reads: 276957
- reads: 242994

+ reads after collapsing: 276957
- reads after collapsing: 242994

stacks collapsed: 0
reads in collapsed stacks: 0

-------------------------
contig: chr2

+ reads: 191295
- reads: 165159

+ reads after collapsing: 191295
- reads after collapsing: 165159

stacks collapsed: 0
reads in collapsed stacks: 0

-------------------------
contig: chr3

+ reads: 175055
- reads: 158148

+ reads after collapsing: 175055
- reads after collapsing: 158148

stacks collapsed: 0
reads in collapsed stacks: 0

[steven]

I am observing a similar trend when looking at non directional RNA-seq data. And that reminds me of a similar post.
If anyone has an idea, i am also interested..

[tujchl]

thanks for your replying steven

[tonybolger]

HI:
I use quest to analysis my chip-seq data, after collapsing reads I found on every chromosome, reads on plus strand are more than on minus strand (example are below), Does it indicate some problem? (I filter out redundant reads before quest)
thank you in advance

This would make me suspicious about the bioinformatic side of the process. While local biases of all kinds can be expected in sequencing, there shouldn't be this kind of systematic bias.

Could you reverse-complement the reads and/or the reference, and then see if the alignment bias swaps in each case?

[tujchl]

Thank you tonybolger, I will try what you said and feedback as soon as possible