Questions tagged [fastqc]
The fastqc tag has no usage guidance.
13
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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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184
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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".
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- 13
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117
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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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52
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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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64
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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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99
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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
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1
answer
50
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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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274
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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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293
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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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841
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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 ...
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4
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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: ...
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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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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 ...
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