Trim WGA reads

[mdelucas]

Hi

I have performed a ChIP followed by WGA (WGA2 sigma), the library worked well, the sequencing fastq looks good. Now I am trying to find the best way to align my reads to the genome (I will use bowtie). I have used trim-reads to read out of the adaptors and the sequences that contain the sequence from the WGA2 adaptors (this is the consensus I am using: TTGGGTGTGTTTGG), but I am not sure that this is the best approach, as I can see reads with "pieces" of the WGA adapators (probably because of the fragmentase step during library preparation).

Any idea? can Bowtie align well my reads if I don't trim the WGA adaptor?

Thanks

[dpryan]

Presuming that TTGGGTGTGTTTGG is the sequence of the universal priming site that the kit puts on, just tell your trimmer to trim with a minimum overlap of 1bp. Alternatively, you could try using local alignment (you'd need to use bowtie2 or a different aligner altogether as I think bowtie just does end-to-end alignment).