Apologies for my inexperience with bowtie.
I have a series of map files all containing reads with very consistent mapping quality: ~35-40.
If not showing go to https://ibb.co/j1fOza
However, when I map them with a fairly generic bowtie command:
bowtie -t -v 2 -p 8 --solexa-quals hg19 -1 end1.fastq -2 end2.fastq out.map
I get consistently poor alignment rates:
the highest is: reads with at least one reported alignment: 537070 (11.58%)
the lowest is: reads with at least one reported alignment: 53707 (0.01%)
There is no documentation on the experiment specifying whether a primer is present in each of these reads. and I am certain it is hg19.
As you can see from the above picture there there is a dip in quality in the first 5 base pairs of the concerned read. This dip is present in all of the reads that I am studying- I thought to get rid of these using the 'Trimmomaster' tools:
fastq_quality_trimmer -t 36 -i end1.fastq -o end1_trim.fastq fastq_quality_trimmer -t 36 -i end2.fastq -o end2_trim.fastq
However the mappings that resulted from these trimmed reads were consistently even poorer than the originals....
Can anyone critique my use of bowtie to see if I can fix this?