After aligning paired-end reads to a reference genome, I am getting low percentage:
34636166 + 0 in total (QC-passed reads + QC-failed reads)
34346076 + 0 primary
0 + 0 secondary
290090 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
5706057 + 0 mapped (16.47% : N/A)
5415967 + 0 primary mapped (15.77% : N/A)
34346076 + 0 paired in sequencing
17173038 + 0 read1
17173038 + 0 read2
3807784 + 0 properly paired (11.09% : N/A)
3996748 + 0 with itself and mate mapped
1419219 + 0 singletons (4.13% : N/A)
177284 + 0 with mate mapped to a different chr
65388 + 0 with mate mapped to a different chr (mapQ>=5)
What has to be done to increase the mapping percentage?
I'm attaching the fastqc report before trimming and after trimming too first- R1 without trimming second- R2 without trimming
third- forward paired fourth- reverse paried
rest are overrepresentations
After using trimmomatic the quality is getting more bad and even the mapping is of low percentage
Mash screen result in the last image
mash screen
2) wrong/bad reference genome (you will know better how to do this, maybemash screen
the reference genome against the screen database?) 3) sample swaps of your library. I don't really have more to say than that. $\endgroup$