Regarding using a W303 reference sequence for read alignment, none of the available references seem good for alignment. As far as I know the W303 sequences are never perfect and contain undefined nucleotides (e.g containing the letter 'N' instead of either of the four nucleotides). Because of this the alignment of our sequencing reads will not be as good as it would be with the S288C reference sequence. S288C is extensively sequenced and does not contain any undefined sequences making aligning more reliable. According to Benoit it is fine to use the S288C reference for cells of the W303 background. The difference between the W303 and the S288C is not very big, so using S288C might be fine to use.
Regarding using a W303 reference sequence for read alignment, none of the available references seem good for alignment. As far as I know the W303 sequences are never perfect and contain undefined nucleotides (e.g containing the letter 'N' instead of either of the four nucleotides). Because of this the alignment of our sequencing reads will not be as good as it would be with the S288C reference sequence. S288C is extensively sequenced and does not contain any undefined sequences making aligning more reliable. According to Benoit it is fine to use the S288C reference for cells of the W303 background. The difference between the W303 and the S288C is not very big, so using S288C might be fine to use.