Hi,
I have used Bowtie2 to map my reads to my genome. The reads are similar to ChIP seq reads. I filtered my reads for a MAPQ score > 10. When I look at the alignments using IGV, reads with a very high MAPQ score (say, 42 for example), seem to not match very well at all on the base-pair level for the genomic regions of interest I'm looking at (regulatory regions). How can this be? Doesn't a high MAPQ score from Bowtie2 mean it is certain that read maps there?
My Bowtie command:
bowtie2 --phred33 --fr -I 100 -X 500 -p 8 --seed 123 -q -t -x Sea_Urchin_Bowtie2_ref_index -1 clean_R1.fastq -2 clean_R2.fastq -S Sea_Urchin_sample_1_bowtie2.sam
[IMG][/IMG]
Any suggestions or comments or help?
Thanks!
I have used Bowtie2 to map my reads to my genome. The reads are similar to ChIP seq reads. I filtered my reads for a MAPQ score > 10. When I look at the alignments using IGV, reads with a very high MAPQ score (say, 42 for example), seem to not match very well at all on the base-pair level for the genomic regions of interest I'm looking at (regulatory regions). How can this be? Doesn't a high MAPQ score from Bowtie2 mean it is certain that read maps there?
My Bowtie command:
bowtie2 --phred33 --fr -I 100 -X 500 -p 8 --seed 123 -q -t -x Sea_Urchin_Bowtie2_ref_index -1 clean_R1.fastq -2 clean_R2.fastq -S Sea_Urchin_sample_1_bowtie2.sam
[IMG][/IMG]
Any suggestions or comments or help?
Thanks!
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