Hi everyone
Our group has recently sequenced 8 RADtag libraries on Illumina HiSeq 2500.
7 of the lanes were very good but one of them was a complete failure. Even though the cluster density was good (~650k/mm2), most of them failed the filter. The 47 million reads we recieved were of very bad quality: 60% of them had an uncalled base (N) at the 7th position and after ~40 bp the quality drops below Phred score 10.
The library had a good concentration and fragment length distribution.
We have no clue what may have gone wrong and we would be very happy for any hint. I have attached some more information, FastQC and SAV plots.
Thanks a lot in advance for any help!
Best,
Joana
Our group has recently sequenced 8 RADtag libraries on Illumina HiSeq 2500.
7 of the lanes were very good but one of them was a complete failure. Even though the cluster density was good (~650k/mm2), most of them failed the filter. The 47 million reads we recieved were of very bad quality: 60% of them had an uncalled base (N) at the 7th position and after ~40 bp the quality drops below Phred score 10.
The library had a good concentration and fragment length distribution.
We have no clue what may have gone wrong and we would be very happy for any hint. I have attached some more information, FastQC and SAV plots.
Thanks a lot in advance for any help!
Best,
Joana
Comment