Questions tagged [fastqc]
The fastqc tag has no usage guidance.
16
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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 ...
- 31
2
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1
answer
94
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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 ...
- 151
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397
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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 ...
- 249
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2
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366
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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:
...
- 13
0
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1
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329
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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".
...
- 13
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159
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fastqCleaner failing to launch in RStudio
When I execute:
> FastqCleaner:::launch_fqc()()
I get the following output
...
- 11
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3
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76
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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 ...
0
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76
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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 ...
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0
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167
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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....
1
vote
1
answer
74
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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 ...
- 107
1
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1
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469
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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 ...
- 107
2
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361
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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
- 127
2
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1
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1k
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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 ...
- 221
4
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2
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3k
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"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: ...
- 43
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4
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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 ...
Ryan Carter
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1
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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 ...
- 2,739