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  • 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

  • #2


    Can open whatever size.

    Comment


    • #3
      Vim for Windows will work. It's good if you also want to search in the file with regular expressions.

      Comment


      • #4
        Thanks u for information

        Comment


        • #5
          Ultra Edit will work.

          It can open any type of file.

          Comment


          • #6
            Thanks you

            Comment


            • #7
              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; 01-07-2013, 12:16 AM.

              Comment


              • #8
                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.

                Comment


                • #9
                  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?

                  Comment


                  • #10
                    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.

                    Comment


                    • #11
                      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

                      -----------------------------------------------
                      Last edited by gsgs; 01-07-2013, 08:35 AM.

                      Comment


                      • #12
                        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,

                        Comment


                        • #13
                          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

                          Comment


                          • #14
                            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

                            Comment


                            • #15
                              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

                              Comment

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