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
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
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