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
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
Comment