I am using the galaxy tool "Stitch MAF blocks" to extract multiple alignments (using the 28-way multiZ) and concatenate them into a single sequence per species. I have noticed that the resulting hg18 sequence in the fasta file contains no gaps (even though there are gaps within the individual blocks). For my downstream applications I need to keep these gaps.
Does anyone know if there is a way with this tool to keep the gaps? Alternatively, can anyone suggest another approach that might solve this problem.
Many thanks in advance,