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
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
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