Dear galaxy users,
       I am trying to map some multiplexing bisulfite PCR data (Illumina) to 
our 20+ genes of interest. I want to use the "Map with Bowtie for Illumina" in 
Galaxy. Therefore, I need to change the reference genome to my known DNA 
sequences. However, I don't know how to make such a reference index. Shall it 
be in FASTQ, FASTA or CTF format? My reference sequences are now in a word 
file. How can I convert their format to the desired one?
      My second question is that my sequencing data for an individual sample 
are separated in 8 different FASTQ files. Does it matter that I map them 
individually and then merge them together? Or shall I combine them first (which 
will be a very huge file) and then do the mapping? Does it change the results 
either way?
      My last question is that since we are looking at the CG methylation, 
there certainly will be mismatches in the CG sites (such as being a CG or TG) 
compared to the reference sequence. I am afraid the mismatches may be greater 
than 3 for a read about 100 bp. Do you think Bowtie will allow these many 
mismatches? If so, can you suggest a better way to do the mapping?

Thanks for your attention!!!

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