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Old 01-04-2013, 10:47 PM   #1
afiroz
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Exclamation can any body say how to see large fastaq file by any editor/program on windows

Dear All,

Please let me know how to see large fastaq file by any editor/program on windows

thanks
firoz
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Old 01-05-2013, 08:22 AM   #2
xied75
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http://mh-nexus.de/en/hxd/

Can open whatever size.
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Old 01-06-2013, 03:00 PM   #3
Dario1984
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Vim for Windows will work. It's good if you also want to search in the file with regular expressions.
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Old 01-06-2013, 10:32 PM   #4
afiroz
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Thanks u for information
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Old 01-06-2013, 10:36 PM   #5
jenyen63
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Ultra Edit will work.

It can open any type of file.
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Old 01-06-2013, 10:42 PM   #6
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Thanks you
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Old 01-06-2013, 11:08 PM   #7
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Quote:
Originally Posted by xied75 View Post
http://mh-nexus.de/en/hxd/

Can open whatever size.

how to switch to normal nonhex display

---------------------------------------

what, if I nondeliberately violate the terms and conditions ?
e.g. I like to put those executables into my utilities folder and then
archive them and copy to another machine.
I can't handle all the licence and readme files in that folder.

Nor can I remember hundreds of different terms and conditions for years

my current editor is from the early 90s , it can't handle files > ~100KB
I use wordpad for those, but it sometimes loads slowly or crashes
and is less comfortable for e.g. editing C-programs

Last edited by gsgs; 01-06-2013 at 11:16 PM.
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Old 01-07-2013, 03:43 AM   #8
GenoMax
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Since you planning to do this on a windows machine I would first suggest making a copy of your fastq file. Just in case.

You can certainly open large files using one of the suggested programs but depending on RAM available (and size of the temp directory) you could potentially have problems trying to view/edit very large files on windows.
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Old 01-07-2013, 06:19 AM   #9
kmcarr
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Quote:
Originally Posted by afiroz View Post
Dear All,

Please let me know how to see large fastaq file by any editor/program on windows

thanks
firoz
While others have given you suggestions which will work, I am wondering why you would want to do this? I am assuming by "large fastaq [sic] file" you mean the output from an Illumina HiSeq. These files have potentially hundreds of millions of individual read/quality entries. What are you planning on "seeing" in this file?
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Old 01-07-2013, 07:01 AM   #10
xied75
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Quote:
Originally Posted by gsgs View Post
how to switch to normal nonhex display

---------------------------------------

what, if I nondeliberately violate the terms and conditions ?
e.g. I like to put those executables into my utilities folder and then
archive them and copy to another machine.
I can't handle all the licence and readme files in that folder.

Nor can I remember hundreds of different terms and conditions for years

my current editor is from the early 90s , it can't handle files > ~100KB
I use wordpad for those, but it sometimes loads slowly or crashes
and is less comfortable for e.g. editing C-programs
HxD always show hex, the right hand column is the normal view.

I have been using HxD for a year, never worried about terms etc. Did you find anything alarming? I once emailed the author to say that he can further develop this program into a very nice Bioinfo tool, never got reply though. I don't think there is anything similar like this out there. Extremely useful to look at sam/bam/gz, open 50GB or 100GB file in 0.1 sec, scroll to anywhere you want, search, compare, etc.
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Old 01-07-2013, 07:29 AM   #11
gsgs
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I had been using list.com, my version from 1994 only displays the first
20MB, though. And no editing.
But it lets you easily switch from hex-mode to normal mode
(Windows XP, 32bit)
-----------------------
searching ...
Vern Buerg, who developed the LIST.COM utility for DOS, passed away
in December of 2009
http://www.bizer.com/zblist/
-----------------------------------------------

Last edited by gsgs; 01-07-2013 at 07:35 AM.
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Old 01-07-2013, 09:40 AM   #12
swbarnes2
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I use vim for Windows too, but really this isn't something you should routinely be doing. You should be gzipping your fastqs. I know bwa can take them just like that, for other programs, you might need to slap a zcat and pipe at the start, but it's much better to leave your files compressed.

In unix, you can check the top of your fastqs with head. So if your file is gzipped, you can do

Code:
zcat my.fastq | head -n 20
to see the top 20 lines, if you want to see how many bases are in the reads, or what the format of the read names are,
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Old 01-16-2013, 07:08 AM   #13
sisch
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Even though the thread is essentially solved, I'd like to add I am using notepad++ http://notepad-plus-plus.org/ whenever I am working on a windows machine.
Besides opening Files of whatever size (personally tested 25GB) it is an extendible text editor that can load a bunch of modules.

Just my two cents.

Simon
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Old 01-16-2013, 07:44 AM   #14
xied75
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Quote:
Originally Posted by sisch View Post
Even though the thread is essentially solved, I'd like to add I am using notepad++ http://notepad-plus-plus.org/ whenever I am working on a windows machine.
Besides opening Files of whatever size (personally tested 25GB) it is an extendible text editor that can load a bunch of modules.

Just my two cents.

Simon
Notepad++ is my first choice also. But you do mean a 64 bit version right? Normal 32 bit can't even open 12GB SAM file.

Best,

dong
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Old 01-16-2013, 11:58 PM   #15
sisch
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Quote:
Originally Posted by xied75 View Post
Notepad++ is my first choice also. But you do mean a 64 bit version right? Normal 32 bit can't even open 12GB SAM file.
Yes, I was speaking of 64bit. My assumption was that in the field of NGS no one would still run 32bit.
Maybe I'm wrong ... don't know ...

Simon
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Old 01-17-2013, 02:01 AM   #16
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Quote:
Originally Posted by sisch View Post
Yes, I was speaking of 64bit. My assumption was that in the field of NGS no one would still run 32bit.
Maybe I'm wrong ... don't know ...

Simon
1, Then the URL you gave doesn't have 64 bit downloading there, which confuses me.

2, In the field of NGS lots of people still don't able to tell the difference between 32 bit OS and 64 bit. When I did my porting of samtools to X64, people complain that it doesn't run on their Windows.

Best,

dong
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Old 01-17-2013, 03:34 AM   #17
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Quote:
Originally Posted by xied75 View Post
1, Then the URL you gave doesn't have 64 bit downloading there, which confuses me.
Sorry for the confusion, I have to withdraw my suggestion of using Notepad++ for large files. It seems my mind extrapolated too much of my memory I checked back on my windows machine (which I'm not using too often):
1) Notepad2 was the 64bit program I had in mind.
2) But Notepad2 doesn't open large files either (I also found Vim for windows installed, so I think I used that for the 25GB file I mentioned)
3) Notepad++ was on my mind, because I did all the downstream stuff with it (opens files up to ~700MB).

Quote:
Originally Posted by xied75 View Post
2, In the field of NGS lots of people still don't able to tell the difference between 32 bit OS and 64 bit. When I did my porting of samtools to X64, people complain that it doesn't run on their Windows.
I have to keep that in mind.
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Old 01-18-2013, 01:29 PM   #18
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I have used LTP Viewer, if you want to quickly view a large file as well as search within it, but not much as an editor.

http://www.swiftgear.com/ltfviewer/features.html
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