Reference Assembly with Ambiguous Chromosomes

[doc2r]

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

[westerman]

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.

[doc2r]

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?

[biznatch]

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.