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Fastq software/programs
Hello, so I have a simple question, what programs can you use to open and read FASTQ files?
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Fastq files are text. So in principal you can use a text editor to open the file (or use cat/more utilities to look at the contents).
In general you will want to do QC/Trimming/Pre-processing/Alignments using the fastq files to do secondary data analysis. -
And some of the programs for QC/Trimming/Pre-Processing/Alignments and secondary data analysis are? Thank you very much btw, it's really appreciated.Comment
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There are links for each of the programs in my post above. If you do not see them then temporarily disable "no script" or any other similar plugin that you may be using to see the links.
QC: http://www.bioinformatics.babraham.a...ojects/fastqc/
Trimming: http://www.usadellab.org/cms/?page=trimmomatic
Pre-processing: http://en.wikibooks.org/wiki/Next_Ge...Pre-processing
General Analysis: http://en.wikibooks.org/wiki/Next_Ge...cing_%28NGS%29Comment
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This is exactly what I was looking for today, thanks again!Comment
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Hi FredTam1,
You can open and read your FASTQ files in any linux based platform or Mac OS systems through the terminal.
you can use either cat filename
or
vi filename
FASTQ files are usually big sized, so you need not &/ not required to read the entire file.
Good luck ahead.Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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