Hey there,
I'm currently doing basic analysis for 3 different ChIP-seq experiments, i.e.mapping (using BWA) and peak calling (MACS). All 3 samples have been processed at the same time, give approx.38million reads each (131bp reads) and the sequence quality is the same (not extremely good but alright after trimming).
BUT, when I mapped the reads to the genome (b37), only 2% of the reads of one sample map, while I get approx.85% mapped reads with the other two samples. 2 % ???!!
How can that happen? Any suggestions what went wrong or where the problem is? Just by looking at the sequence reads in the fastq file I can't see any problems... Any help highly appreciated!!!!
I'm currently doing basic analysis for 3 different ChIP-seq experiments, i.e.mapping (using BWA) and peak calling (MACS). All 3 samples have been processed at the same time, give approx.38million reads each (131bp reads) and the sequence quality is the same (not extremely good but alright after trimming).
BUT, when I mapped the reads to the genome (b37), only 2% of the reads of one sample map, while I get approx.85% mapped reads with the other two samples. 2 % ???!!
How can that happen? Any suggestions what went wrong or where the problem is? Just by looking at the sequence reads in the fastq file I can't see any problems... Any help highly appreciated!!!!
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