GFF file formatting

[naluru]

Hello,

I downloaded some GFF files from ensembl website and only need a small subset of rows in these files. So, I opened them up in Excel and chose whatever I wanted.

I saved them as tab delimited text files and everything looked ok. But, I am having trouble with downstream analysis.

My question is, are there any software to check the formatting of my edited GFF files? If so, I will be really happy if you could share them with me.

Also, is there any better way to edit GFF files than opening them in Excel. I heard line endings could also cause some problems between Mac and Linux.

Thank you,
Neel

[joscarhuguet]

There are some tools for manipulating gff files;
If you have a little of experience with perl you could use them.

http://biowiki.org/GffTools#GFF_tools

[steven]

Also, is there any better way to edit GFF files than opening them in Excel.

If you are on linux you can edit text files using grep, gawk, sed, perl, etc.
There are nice linux tutorials around.

I heard line endings could also cause some problems between Mac and Linux.

I tried this:

http://www.google.com/search?hl=en&source=hp&biw=1211&bih=590&q=dos2unix+mac&aq=2&aqi=g10&aql=&oq=dos2unix

http://www.google.com/search?hl=en&safe=off&biw=1211&bih=590&q=mac2unix&aq=0sv&aqi=g-sv1&aql=&oq=mac2lin

[rudi283]

I've tried to do something similar with gff file and it works fine for me. Just need to make sure that the information in each column in excel spreadsheet is ok. I coppied it into 010 Editor and saved as a gff file(I did it only because I had too many rows to put it all into one spreadsheet).

[steven]

Another reason why opening an annotation file with Excel should be avoided: gene names can be automatically changed

[ge_SF]

Quick way to tell if it is an end of line issue - if you type: more my_file from the command line you will see the funky EOL characters that you won't necessarily see just opening the txt file.

There are methods to fix the problem, but I agree with steven that the best thing is to do it in unix. Most likely grep is what you need (to select certain rows, based on whether they have the pattern you are looking for). cut may also be useful- this will select by column. There are plenty of online guides for these.