Per base sequence content warning in ChIPseq data FastQC analysis

Please suggest me what should I do in such case and what tool would be appropriate for downstream analysis? Per base sequence content error in chipped sample FastQC analysis

chip-seq fastqc

• 460 views • link

updated 3.3 years ago by Ram 4.5K • | written 3.4 years ago by shashianand15 0

0 answers

No answers yet.

More posts like this

FASTQC: per base n content fail
written 2.2 years ago by Eddie 0

Hey, guys! I'm processing some whole-genome sequencing data, and some reported "per base n content" fail. I'm wondering that how the fail influencing SNV calling, …
Per base sequence content error in RNAseq analysis
written 2.4 years ago by ahmad.sajad4541 0

i am new to rna-seq analysis. i have downloaded paired end data from SRA database and upon checking these data through FASTQC it is showing …
Illumina reads to be processed and prepared for reference genome alignment
written 2.7 years ago by Veselina 0

Hello to all! I have to align sequence reads obtained by Illumina HiSeq/Nova to a reference genome. The sequencing was carried out using 2x150 paired-end …
Per sequence GC content graph showing two peaks in ChIPseq data analysis
written 3.4 years ago by shashianand15 0

Please help me to understand what is this another peak? I am getting this peak in my chipped and input (slightly lower) samples. what tool …
Fastqc lsequence duplication and per base sequence content failed
written 3.5 years ago by waqaskhokhar999 16

I have around 150bp, paired-end RNA-seq data of 321 samples with around 30 Million reads per sample and I am interested in quantifying the expression …
fastqc: Per base sequence content
written 3.6 years ago by khoojj 2

Hi all, I've seen many posts and questions regarding the error flagged by fastqc on "Per base sequence content". My understanding is the variation at …
Biased GC content distribution in miRNA Illumina sequencing data
written 4.3 years ago by madhuratathode 0

Hi All, I am working on small RNA (miRNA) sequencing data analysis of human Glioblastoma cell line. I am checking the fastqc analysis results for …
Per base sequence content failed in fastQC
written 4.9 years ago by yliueagle 29

In the fastQC report of my ChiPseq (paired-end, H3k27me3, Sanger / Illumina 1.9, Sequence length: 42), I got failure in **Per base sequence content** (see …
Per sequence GC content still not good after trimming
written 5.0 years ago by zouini6 0

I am analyzing NGS data for a prokaryotic genome and FastQC initially failed "Per sequence GC content". I then ran Trimmomatic on my Fastq files …
how to remove warning and failures observed inQuality report by Fastqc for RNA-Seq data
written 7.5 years ago by aiswaryabioinfo 3

Hi All, I ran FastQC software on RNA-Seq data of Plant sample generated from illumina HiSeq platform. It all appears good (green) except : **In …