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3.9 years ago
ashwin.koppayi
•
0
Hello,
I am analyzing human RNA Seq data from a paper (PRJNA421274). I did FastQC on the RAW data and it showed high difference between %A and %T as shown in the link below
Even after trimming it is the same.Is it unsusal and should i use this samples? Is there a way to reduce this difference? I am new to RNA Seq Analysis.Any help is appreciated!
Thank you in advance.
Don't bother too much with fastqc. Trim adapters and align the data, then see if you get a good mapping rate and if most reads align to exons, that is the more relevant QC than fastqc itself.
Thank you for the prompt response. I aligned trimmed samples using STAR using the default options but number of uniquely mapped reads is quite low less than 10% and high %unmapped:too short. I tried to tweak this as suggested in (https://github.com/alexdobin/STAR/issues/169) but it is still too low.
How did you trim?
I used Trimmomatic