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Old 08-29-2013, 03:26 PM   #1
FredTam1
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Question 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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Old 08-29-2013, 04:46 PM   #2
GenoMax
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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.
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Old 08-29-2013, 04:50 PM   #3
FredTam1
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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.
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Old 08-29-2013, 04:53 PM   #4
GenoMax
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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%29
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Old 08-29-2013, 04:58 PM   #5
FredTam1
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This is exactly what I was looking for today, thanks again!
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Old 08-29-2013, 09:30 PM   #6
vishnuamaram
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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.
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