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Suggestions on software used to open large text files

Bioinformatics NGS Software large text files

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4 replies to this topic

#1 marek82313

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Posted 22 January 2014 - 11:01 AM

Dear all,

 

me and my lab-mates have just started working with next-generation sequencing (ChIP-Seq). One colleague of mine need to open very large text files containing ChIP-seq sequences, he generated this file using Galaxy tools but need to open it in local. Which software do you suggest to use to open it? Up to now, he is using Sublime Text 2, but seems that he is able to open just a fraction of the entire file. We are working with Mac-based machines.

 

Thanks,

 

Marco



#2 pcrman

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Posted 22 January 2014 - 11:22 AM

I don't know any mac program, but for PC, textpad can open large text files. Alternatively, you can install virtual Linux OS in Mac OS. 

 

#3 bob1

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Posted 22 January 2014 - 11:29 AM

Try Vim - it's already bundled with all OS-X and higher versions.  Just open a terminal (applications>utilities) and type vim, then hit enter.



#4 mboss

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Posted 22 January 2014 - 01:52 PM

Depending on what you want to do, command line tools such as sort, head and awk might be useful (these are installed by default on Mac and Linux), for example if you just need to filter and/or sort the data.



#5 El Crazy Xabi

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Posted 22 January 2014 - 04:39 PM

In windows I use Notepad++, though I haven't been able to open really big files from Illumina sequencing (before I knew you don't need to).

You have a list of similar programs for Mac here







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