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8 votes
Accepted

Why don't all reads have adaptors?

Things like this might depend on your specific library prep, but in general: sequencing starts at the end of the adapter, not before it. You will only see adapters if you sequence through the entire ...
Wouter De Coster's user avatar
6 votes
Accepted

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

To answer your direct question, there are a few reasons why there might be high levels of sequence duplication. From the FastQC help: The underlying assumption of this module is of a diverse ...
Daniel Standage's user avatar
6 votes

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

FastQC assumes that all samples are for whole genome sequencing and will flag them as failed if they differ too much from that assumption. This will, for example, cause essentially all RNA-seq, ChIP-...
Devon Ryan's user avatar
  • 19.7k
5 votes

Bash scripting FastQC for multiple fastq files in multiple directories

multiqc kind of glazes over some important information, like the exact adapters and duplicated sequences in a library. If you plan to spend big $$ for sequencing a ...
conchoecia's user avatar
  • 3,181
3 votes

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

Yes, reported accuracy can be tested and compared with actual accuracy by mapping reads from a reference sample to a known-perfect reference sequence. It's usually done in aggregate, at a read level ...
gringer's user avatar
  • 14.4k
3 votes

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

On a regular basis, using FastQC is quite enough as to assess the quality of FastQ-formatted data. It gives you plenty of details as can be seen in the screenshots you shared. As others have commented ...
JRodrigoF's user avatar
  • 827
2 votes

Bash scripting FastQC for multiple fastq files in multiple directories

This is the typical kind of job for snakemake. Assuming your have one file per replicate named for instance T9/Infected/Rep1/Rep1.fastq.gz, you can prepare a file ...
bli's user avatar
  • 3,130
2 votes

fastqCleaner failing to launch in RStudio

The issue is with the navbar page, downgrading shiny to 1.6 or in my case 1.4 fixed it for me, the detailed link to find to the solution is here: https://github.com/rstudio/shiny/issues/3556 Cheers.
adeizadavid's user avatar
2 votes

SyntaxError after end of Snakefile code?

How to figure out what error messages are trying to tell you is one of the great mysteries… :-) What version of Snakemake are you using? I get slightly different messages. With an ancient version (3....
John Marshall's user avatar
2 votes
Accepted

Per Base Sequence Content in fastqc

The positions you see in the x-axis of this plot are positions on your reads, not on the reference genome. Since each read comes from a random position on the genome, the frequency of A/T/C/G on each ...
PedroSebe's user avatar
  • 216
1 vote

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

Cross-posted and answered on biostars: https://www.biostars.org/p/9583849/#9583850 https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR20708369&display=metadata is a 10x single-...
Ram RS's user avatar
  • 2,425
1 vote

SyntaxError after end of Snakefile code?

You're missing a comma between the two output lines. (John Marshall's more detailed syntax error message was spot-on.) With a simplified version of your Snakefile: ...
Jesse's user avatar
  • 947
1 vote
Accepted

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

From a quick look at the manual, it looks like you are supposed to use just the wrapper, not combine the wrapper with a ...
Ram RS's user avatar
  • 2,425
1 vote

Genome QC + Assembly Pipeline semantics

Maybe take a look at workflow management systems, like snakemake Nextflow Toil Cromwell Admitted, each of those adds their additional learning curve. However, especially snakemake is not so much ...
Carambakaracho's user avatar
1 vote

Warning in fastqc

Generally yes, but it depends the type of study. Remember that Fastqc was developed for bacterial genomes, mainly, so an unusually shaped distribution in that particular dataset could indicate a ...
zorbax's user avatar
  • 769
1 vote

What pitfalls exist with running FastQC on a bam file?

I don't see why you are trying to compare two totally different measurements. When FASTQC says a read is unique, it means that no other read shares its sequence. When STAR says a read is uniquely ...
swbarnes2's user avatar
  • 1,941

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