I did a run using miseq (v3 chemistry, paired end 2x300, 25% PhiX added). I did a own designed pcr based library preperation.
Now for some of the samples on the flow cell I get very strange sequences that dont fit what I am expecting. After running it through some aligments i noticed that the sequences all are PhiX sequences (Enterobacteria phage S13, Scaffolding protein D, Protein F ect.)
The samples
As I am quite new to the field of sequencing and havent had this befor I was wondering:
1. Does the PhiX library also contain an Index? (And could it be that I by chance gave this index to my samples thus mixing the sequences I want with lots of PhiX sequences)
2. If that is not the case: Why does the Miseq give me the sequences? (I used a sample sheet and specific Indexes.) How can something without an Index be exporter?
3. Those samples did not produce a lot of reads (about 6000-60 000). Possibly my preperation did not add the adapter correctly to those samples and only surrounding noise from the high concentration of PhiX was measured?
Thanks for any advice
Now for some of the samples on the flow cell I get very strange sequences that dont fit what I am expecting. After running it through some aligments i noticed that the sequences all are PhiX sequences (Enterobacteria phage S13, Scaffolding protein D, Protein F ect.)
The samples
As I am quite new to the field of sequencing and havent had this befor I was wondering:
1. Does the PhiX library also contain an Index? (And could it be that I by chance gave this index to my samples thus mixing the sequences I want with lots of PhiX sequences)
2. If that is not the case: Why does the Miseq give me the sequences? (I used a sample sheet and specific Indexes.) How can something without an Index be exporter?
3. Those samples did not produce a lot of reads (about 6000-60 000). Possibly my preperation did not add the adapter correctly to those samples and only surrounding noise from the high concentration of PhiX was measured?
Thanks for any advice
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