I have a question about the alignment of chip-seq data.
I have got sample with 100 bp reads. After QC and trimming, these got shorter. I used bowtie to do the alignment. I got lots of warning message like
Warning: Skipping read (myData.110237305 VADER:39:C0NL4ACXX:1:2316:19783:100655 length=101) because it had length 0
What does this warning message mean? and how can i overcome it? is there an option in bowtie that will deal with this? (i check the options but could not see one!)