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seq_lover 11-18-2011 07:46 AM

some basic queries (mapping)
 
Hi everyone,

I am newbie to sequencing analysis. I would be thankful if someone can answer these questions:-

1) What are uncallable bases in reads? Are these "N" thing in some reads. Because when I read any article it says we should remove reads with uncallable bases.

2) There are two types of reference genome you can map against. One is with repeats and other is without repeats. Which one I should use for reads from DNA sequencing? Also, will it change if I have data from RNAseq?

3) I used Whole genome including intergenic and introns and mapped my RNAseq data against it. The reads were paired and in the end I found that only 20-30 % of my paired reads were mapped correctly(same distance apart as of insert size). I am sure as i RNAseq reads there is a possibility of getting this type of result. But is the number correct. Also, is there any way you can be sure that mapping was done in correct way.

Thanks


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