Questions tagged [fastqc]

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Fastq file with very high per base sequence quality and no box-whisker plot

I have my data from NCBI. I am having difficulty making sense of and correlating my fastq file read 1 and read 2 and the fastQC report. As shown below, I have two paired-end read results each ...
Pumla 's user avatar
3 votes
0 answers
134 views

Mean and median identical with no variation in FASTQC results

Mean and median identical with no variation in FASTQC results After using FASTQC, in the section of "Per Base Sequence Quality" I encountered a problem when I saw the Box & Whisker type ...
yahya jand's user avatar
2 votes
1 answer
122 views

Can we test the accuracy of Phred scores shown in FASTQ files

Recently I have ran a human WGS on the BGI DNBSEQ system, and their FASTQ quality scores seem to be quite impressive, where the Phred scores barely deteriorate along the read length when checked on ...
benson23's user avatar
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2 votes
1 answer
657 views

If fastp output is not a good measure of FASTQ correctness, what is?

In the beginning of my pipeline, I just fed the paired reads (2 files) into fastp, with the default options, and assumed it would do a good job preparing the reads for the next step: alignment But I ...
gl00ten's user avatar
  • 249
1 vote
2 answers
439 views

SyntaxError after end of Snakefile code?

I am trying to run Fastqc on multiple files using Snakemake but am receiving an ambiguous SyntaxError past the last line of code in the Snakefile. Snakefile: ...
Swietenia's user avatar
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1 answer
359 views

Snakemake Fastqc: "Multiple run or shell keywords in rule run_fastqc."

I am trying to check the quality of RNA-Seq data from Illumina using fastqc in snakemake in a conda environment. I get the error "Multiple run or shell keywords in rule run_fastqc". ...
Swietenia's user avatar
1 vote
1 answer
163 views

fastqCleaner failing to launch in RStudio

When I execute: > FastqCleaner:::launch_fqc()() I get the following output ...
Leon Lenzo's user avatar
0 votes
3 answers
77 views

Genome QC + Assembly Pipeline semantics

I’m trying to create a pipeline for genome assembly. How best can I “redirect/pipe” from existing fasta files (or files in general) to other steps of the pipeline? I was thinking of going from the SRA ...
user10415's user avatar
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0 answers
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FastqCleaner in R, not recognizing paired-end fastq file?

I've recently downloaded the FastqCLeaner to process paired-end fastq files locally using R (4.0.3). I'm having trouble with the shiny app. It is not uploading my second fastq file, and is repeated ...
Najeha Mohamed's user avatar
1 vote
0 answers
206 views

FastQC and Trimmomatic in Galaxy?

I am independently working on data retrieved SRA database, paired-end data as separate inputs. The proceedure I followed is, After running FastQC using Galaxy, the majority of the modules have failed....
Najeha Mohamed's user avatar
1 vote
1 answer
87 views

Warning in fastqc

I am checking the quality control of my sequences using the Fastqc tool. For some steps, like "Per base GC content", etc., I received a warning. So, I was wondering whether I Should also take care of ...
Negin's user avatar
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1 vote
1 answer
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Per Base Sequence Content in fastqc

I have a question regarding "Per Base Sequence Content" plot for "fastqc": In the fastqc documentation, it is written: "In a random library you would expect that there would be little to no ...
Negin's user avatar
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2 votes
1 answer
399 views

Why don't all reads have adaptors?

I got NGS reads back from sequencing platform. I check for adaptors and trimmed them. But I realized only a fraction (eg 30%) have adaptors... why not all of them? Thanks
LauraR's user avatar
  • 127
2 votes
1 answer
1k views

What pitfalls exist with running FastQC on a bam file?

I was analysing a bad sequencing run of some RNA data using FastQC, I supplied it RNA-STAR-aligned bam files (and the human reference). The output of MultiQC had many more "unique reads" in ...
hepcat72's user avatar
  • 221
4 votes
2 answers
3k views

"Sequence Duplication Levels" module still fails after pre-processing Illumina data

I want to ask about why the sequence duplication levels are high after I trimmed by using Trimmomatic? I am using the following Trimmomatic operations: ...
yy97's user avatar
  • 43
7 votes
4 answers
9k views

Bash scripting FastQC for multiple fastq files in multiple directories

I am completely new to bioinformatics so I'm looking to learn how to do this. I have multiple directories with fastq files: E.g; 10 Directories with each time series, each with Treatment and control ...
user avatar
1 vote
1 answer
4k views

How to interpret duplication from MultiQC/FastQC?

FastQC of my sample files, aggregated into a single plot by MultiQC. Blue represents unique reads. Black represents duplicate reads. The x-axis is the number of reads. I see I have more duplicate ...
SmallChess's user avatar
  • 2,699