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!!!
Xiefan
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