N base in RNA-seq data
Hi, I do an alignement of RNA-seq publish data with STAR aligner. I see in fastqc that for some sample, N content increase to 12% at base 4 and 22 (warning in orange). Should i cut N part ?
Thanks
• 1,161 views
•
link
written
by
cellulebioinfobiscem •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
why my fastqc on trimmed data failed?
written by kamran.kouchakzadeh.kk •
-
Small secondary peak for per sequence GC content - FASTQC results (bulk RNA-seq)
written by Fossil •
-
FastQC per base to total base calculator
written by jimmy0958073736 •
-
RNAseq fastqc report some failures, how to solve it?
written by lovelymaoqin •
-
STAR Generating Genome Indices error
written by Balatheskulter •
-
how to remove warning and failures observed inQuality report by Fastqc for RNA-Seq data
written by aiswaryabioinfo •
-
Isn't fastq file header suppose to have barcode sequence?
written by salamandra
-
GC content for RNA-Seq data
written by sukesh1411 •
-
FastQC low %A in per base sequence content
written by Duff
-
Quality report by Fastqc, Result Interpretation and Next step parameters
written by ravi.uhdnis
Looks like this data is not good, especially if you consistently have N's at specific cycles. Such data should not have been released by the sequencing facility. You can't remove N's since that will mess up reading frame.
You can filter out reads with N's using
reformat.shfrom BBMap suite by doing:or
(if reads are paired-end).
Thanks you for tools suggestion, I will test it.