Question: Notepad and word will not read Fastq or FASTA files
0
gravatar for paul.sillence
3.6 years ago by
United Kingdom
paul.sillence0 wrote:

Hi,

I am having issues when trying to open a fastq or fasta file in notepad or word. When I open them it just shows an unreadable code e.g. 

8ՙ���;����S>��m����%��7ޱ�a��p��†n�qDx���@�~r����01��@��'��m��5"X�a��5��������x�c��!0������ޞ�
i�ɲ�zWU�.�V�p��u�솦�s�f�a8��d��r^M�mQ�i6��yQL�,o��m:�W�<[M��;LK���r�M8���d]Tk�l�E&!'D)�I��D4� 

and so on!

In turn, the blast software I am trying to run does not recognise the data. I have also tried to open these files on another desktop, in notepad and they display the data as it should be.

I am using a brand new Dell optiplex 7020, with windows 7 pro, Intel i5-4590, 64 bit.

Any help would be much appreciated

fastq reader software error • 2.4k views
ADD COMMENTlink modified 3.6 years ago by Adamc540 • written 3.6 years ago by paul.sillence0
7

You are correct, they won't.

ADD REPLYlink written 3.6 years ago by Neilfws48k
3

In addition to what everyone else has stated already, you'll generally want to avoid Word Processors (especially for data) such as Word.  In addition, the DOS operating system is not really bioinformatics friendly.  You'll want to use a text editor for code and to occasionally look at small data files (generally you would selectively look at FASTA files at the command line).  As far as text editors go, I would recommend both Notepad++ or Sublime Text for your windows system.

ADD REPLYlink written 3.6 years ago by Josh Herr5.6k
1

That's no error, you've discovered extraterrestrial DNA!

ADD REPLYlink written 3.6 years ago by Daniel3.6k
5
gravatar for Michael Dondrup
3.6 years ago by
Bergen, Norway
Michael Dondrup44k wrote:

Most likely your files are compressed. Anyway you shouldn't open your fasta files in Word.

ADD COMMENTlink written 3.6 years ago by Michael Dondrup44k
4

Unless you're using BioWord? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3546851/ ;)

ADD REPLYlink written 3.6 years ago by Daniel Swan13k
6

The mere existence of that tool makes me sad.

ADD REPLYlink written 3.6 years ago by Chris Miller20k
3
gravatar for Adamc
3.6 years ago by
Adamc540
United States
Adamc540 wrote:

If they're actually opening the files at all, I'm assuming they're not so large as to exceed the limits of those programs (as is often the case with notepad and NGS-derived output files). Start with making sure that file extensions are viewable, and make sure that you're not actually trying to open compressed files (usually will end in .gz). You'll need to extract them to view them. If they're up to a couple hundred megabytes, you can open them with Notepad++ in windows (as already mentioned). For larger files, try LTFViewer. It's read-only, but it'll handle opening/searching multi-gigabyte text files in Windows without issue.

And if you're going to be getting into a lot of this stuff, install Linux inside a VirtualBox VM- there are many things that are actually faster/easier/less buggy after learning to manipulate text files with integrated Unix/Linux tools.

ADD COMMENTlink written 3.6 years ago by Adamc540
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