Hi,
I have two sets of Illumina Single End RNA-Seq 50 bp data (two differents days of mammalian cell culture). The kit used was KAPA Stranded RNA-Seq Kit with RiboErase.
Unfortunately the results from FastQC are not as expected. But the problem is that I am not exactly sure how to interpret the data and what to say about the plots.
Both datasets show the same results. The plot of per base sequence quality is OK (I think) and also the plot of Adapter content, but the plots of GC content and Kmer content look very weird. Also, the duplication levels.
I am happy to get any advices about what is wrong in this data or possible explanations for this results.
Thanks for any help
Ileana
First three results of
Overrepresented sequences:
Sequence
CGACGGGGGGCCCCGCGGGGCCGAGAAGAAGAGGAGGGGGAGGCGAGGAGG Count: 187325
Percentage: 1.0857026079582217
Possible Source: No Hit
Sequence GGACAGGAGAGCGGTCGCGCCGTGGGAGGGGCGGCCCGGCCCCCACCGCGG Count: 98598
Percentage: 0.571456590094567
Possible Source: No Hit
Sequence CCCGAGACGAGTGGCTCTCCGCACCGGTCCCCGGTCCCGACGCGCGGCGGG Count: 95732
Percentage: 0.5548457603899987
Possible Source: No Hit
I have two sets of Illumina Single End RNA-Seq 50 bp data (two differents days of mammalian cell culture). The kit used was KAPA Stranded RNA-Seq Kit with RiboErase.
Unfortunately the results from FastQC are not as expected. But the problem is that I am not exactly sure how to interpret the data and what to say about the plots.
Both datasets show the same results. The plot of per base sequence quality is OK (I think) and also the plot of Adapter content, but the plots of GC content and Kmer content look very weird. Also, the duplication levels.
I am happy to get any advices about what is wrong in this data or possible explanations for this results.
Thanks for any help
Ileana
First three results of
Overrepresented sequences:
Sequence
CGACGGGGGGCCCCGCGGGGCCGAGAAGAAGAGGAGGGGGAGGCGAGGAGG Count: 187325
Percentage: 1.0857026079582217
Possible Source: No Hit
Sequence GGACAGGAGAGCGGTCGCGCCGTGGGAGGGGCGGCCCGGCCCCCACCGCGG Count: 98598
Percentage: 0.571456590094567
Possible Source: No Hit
Sequence CCCGAGACGAGTGGCTCTCCGCACCGGTCCCCGGTCCCGACGCGCGGCGGG Count: 95732
Percentage: 0.5548457603899987
Possible Source: No Hit
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