Skipping Reads Bowtie

Question

[roll]

Hi,

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!)

Answer 1

[brentp]

I would guess that your trimmer trimmed some reads so that they have no bases left (length 0). It does not discard them so as to maintain pairing between paired-end reads. If yours are single-end, there is likely an option to discard those. Still, this looks like a warning so removing reads before aligning won't affect your results.

[roll]

Thanks. that make sense. I went through the bowtie parameter options but did not find which one would discard these. Do you know the name or which parameter i should set?