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Old 01-18-2011, 02:35 PM   #1
doc2r
Junior Member
 
Location: Huntington

Join Date: Aug 2010
Posts: 9
Default Reference Assembly with Ambiguous Chromosomes

Hi there,

What are peoples thoughts on using the ambiguous chromosomes in their reference assembly for mapping reads....
for example these....

>chr10_random
>chr11_random
>chr13_random
>chr15_random
>chr16_random
>chr17_random
>chr18_random
>chr19_random
>chr1_random
>chr21_random
>chr22_h2_hap1
>chr22_random
>chr2_random
>chr3_random
>chr4_random
>chr5_h2_hap1
>chr5_random
>chr6_cox_hap1
>chr6_qbl_hap2
>chr6_random
>chr7_random
>chr8_random
>chr9_random
>chrX_random
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Old 01-19-2011, 07:45 AM   #2
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

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No technical problem with using the ambiguous chromosomes; I have done so when required. If you will get any useful information from doing so is a different matter. It depends on your project.
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Old 01-19-2011, 08:08 AM   #3
doc2r
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Thanks for your response westerman,

I question whether we get useful information also. Currently we are doing some WGS. when have you been required to include the ambiguous chromosomes?
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Old 01-20-2011, 09:14 AM   #4
biznatch
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I'm interested in a gene that is on an ambiguous chromosome so I always include all of them when aligning my chip-seq data. I'm using mouse. I get good alignments to some regions on these ambiguous chromosomes.
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