Questions tagged [fastqc]
The fastqc tag has no usage guidance.
13
questions
1
vote
2answers
75 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:
...
0
votes
1answer
70 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".
...
1
vote
0answers
69 views
fastqCleaner failing to launch in RStudio
When I execute:
> FastqCleaner:::launch_fqc()()
I get the following output
...
0
votes
3answers
42 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 ...
0
votes
0answers
42 views
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 ...
1
vote
0answers
74 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....
1
vote
1answer
45 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 ...
1
vote
1answer
175 views
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 ...
2
votes
1answer
283 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
2
votes
1answer
648 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 ...
4
votes
2answers
2k 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: ...
6
votes
4answers
6k 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 ...
1
vote
1answer
2k 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 ...
