Change reads' positions in SAM file??

[Fad2012]

Dear All

I want to modify the reads' position, and the insert size in SAM file. What i did, is that i opened the SAM file with Excel, changed the positions manually, then saved the file. I found out that Excel could not save the file, it could read it only. The reads positions are in column 4 and 8 in the SAM file, and the insert size is in column 9. What is the best way to complete this job?

Many thanks

[mastal]

Using a text editor, or a perlscript, depending on how many entries you are trying to change.

[GenoMax]

It is safe to assume that you are doing this on a PC/Mac.

If you must(/want to) use an editor then try one of the following. If the files are going to be used on a unix machine then remember to save (in unix format).

Windows: http://notepad-plus-plus.org/
OS X: http://www.barebones.com/products/textwrangler/

If the files are very large (GB's) then using programmatic means may be your only option if the above programs can't open your file(s).