Entering edit mode
4.1 years ago
Usama Bakry
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0
Hi!, I have a data (WGS for Klebsiella samples) sequenced on illumina MiSeq and the quality of the sequences is very bad. But when I merged the paired-end reads, I got good quality sequences with some outliers like the attached picture and I don't know how to remove these outliers. So, any help?
How did you do the merging? (which software?)
don't just append read2 to read1, that makes very little sense.
Also, what is the insert size of the library? Looks like quality drops in the later cycles of R1 and R2. From what I know this is not too unusual, but I am unsure what to what extend this is normal. Maybe you are hitting adapter sequences. Does fastqc indicate adapter contamination?
I removed all adapters from R1 and R2 before merging, so I am sure that there is no adapter contamination
I used PEAR to merge the paired-end reads
can you provide the exact PEAR cmdline you execute? (not sure on this, but I seem to remember that PEAR is very liberal when merging reads)
It's hard to see from the graph but what is the max read length of the merged reads? What was actually the original sequencing mode that was done for these samples?