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Old 05-20-2010, 07:42 AM   #1
yh253
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Default hg19 genome reference for short read mapping

Dear all,

I am wondering does anyone use only base genome sequences:chrs1:22, X, Y when does the reads alignment? By excluding chrM, chrUn... etc., it will surely have some effect on the alignment results, but would this be a serious problem?

I actually excluded all these sequences apart from base sequences during my alignment with bowtie/bwa, because we thought we were not very interested in the binding on the mitochondrion sequences, and somehow we could get more alignable reads, but recently we found some of the most duplicated reads in our data have been perfectly mapped to mitochondrion sequences, but with one or two mismatches to the base sequences, which make us to think about whether it is necessary for us to include the chrM into our reference genome. It would be really appreciated if you could shed some light on it! Thank you very much in advance!

Yuan
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Old 05-20-2010, 11:07 PM   #2
john_mu
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It is useful to include chrM so that you know which of your reads are multiply mapped. This could help you assess the reliability of the mapping. Besides, ChrM is quite small so it should not take long to do the mapping.
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Old 12-27-2013, 11:30 AM   #3
arcolombo698
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Hello. I have the same issue here. I am not sure where to find the ChrM reference genome to add to my tophat alignment. I am looking here http://genome.ucsc.edu/cgi-bin/hgGateway
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Old 12-27-2013, 12:27 PM   #4
arcolombo698
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Default ChrM in the reference genome

Quote:
Originally Posted by yh253 View Post
Dear all,

I actually excluded all these sequences apart from base sequences during my alignment with bowtie/bwa, because we thought we were not very interested in the binding on the mitochondrion sequences, and somehow we could get more alignable reads, but recently we found some of the most duplicated reads in our data have been perfectly mapped to mitochondrion sequences, but with one or two mismatches to the base sequences,

***********
which make us to think about whether it is necessary for us to include the chrM into our reference genome. It would be really appreciated if you could shed some light on it! Thank you very much in advance!
***********
Yuan
Yes I am interested in the same issue. And what I have found with the hg19 reference is that it already contains the chrM.fa within the chromosome directory of the hg19. which means that when you run the alignment, if something should be aligned to chrM, it will.

I think that you may not need to add the chrM reference if it is already in the chromosome directory of hg19 (assuming you are studying homo sapiens).

?? is this true?
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Old 12-29-2013, 09:11 PM   #5
yueluo
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Quote:
Originally Posted by arcolombo698 View Post
Yes I am interested in the same issue. And what I have found with the hg19 reference is that it already contains the chrM.fa within the chromosome directory of the hg19. which means that when you run the alignment, if something should be aligned to chrM, it will.

I think that you may not need to add the chrM reference if it is already in the chromosome directory of hg19 (assuming you are studying homo sapiens).

?? is this true?
I'm not sure about this, but a short ' grep ">" your-reference-seq.fa ' command should tell you what's in your reference.
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