Hi all ,
I am new to bioinformatics. I have encountered some problems with the data analysis(RNA-seq for human, Pair-end 101cycle). The per base sequence content and Kmer content look pretty strange from what i expected.
Here are my questions (please use the attached file for reference)
1.There is a sudden rise of %A around 50bp. Would it be adapter contamination? but the adapter content keeps low throughout the whole run.
2. What is the possible cause of the A/T imbalance?
3. What is the possible cause of peaks around 40-49bp from the Kmer content?
4. why the base quality drops after 50bp?
Can anyone give me some clue on these questions, it's been puzzling me for a week.
Thank you
I am new to bioinformatics. I have encountered some problems with the data analysis(RNA-seq for human, Pair-end 101cycle). The per base sequence content and Kmer content look pretty strange from what i expected.
Here are my questions (please use the attached file for reference)
1.There is a sudden rise of %A around 50bp. Would it be adapter contamination? but the adapter content keeps low throughout the whole run.
2. What is the possible cause of the A/T imbalance?
3. What is the possible cause of peaks around 40-49bp from the Kmer content?
4. why the base quality drops after 50bp?
Can anyone give me some clue on these questions, it's been puzzling me for a week.
Thank you
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