Hello Xiefan,
For this type of analysis, using a tool such as Bismark would be best.
http://www.bioinformatics.babraham.ac.uk/projects/bismark/
An open ticket to wrap this tool for Galaxy, that you can follow, is here:
http://bitbucket.org/galaxy/galaxy-central/issue/626/wrap-bismark
For custom genomes in general, help is in our wiki:
http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome
Best,
Jen
Galaxy team
On 5/14/12 9:43 AM, Fang, Xiefan wrote:
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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___________________________________________________________
The Galaxy User list should be used for the discussion of
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at usegalaxy.org. Please keep all replies on the list by
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