Concatenate GFF file

[lellabioinfo]

Dear Users,
I have to align different reads from different patients to find SNP and mutations.
Is there a method to concatenate gff file in a unique gff file? (for example, to run this unique file in Solid Alignment Browser)

Thanx,
Maria Elena

[westerman]

Ah, this question may relate to your previous one which I just answered. Anyway you could do a simple 'cat' concatenation of GFF files to get a single file that can be loaded into the SAB. You may need to get rid of the comment lines (#) in the second and subsequent files. A bigger problem is that the name of the reads in multiple SOLiD runs are not unique. For this you will need some way of renumbering the reads. The time I did something similar to this I had to write a custom program which kept the format of the read name (nnn_nnn_nnn_F3) but substituted a new sequential number for each read. This obviously destroys any back-tracking to the original data but we did not find that to be a drawback.

Anyway there is no off-the-shelf method (that I know about) to combine GFF files from different solid runs so that each read is uniquely identified.

[Sheila]

careful with the file size

Hi,
I'm not sure about the maximum size you can use for the SAB but I think is limited. Your computer might crash if the .gff file is too big.

S.

[westerman]

Sheila is indeed correct that there is a maximum size you can use for the SAB. This is the main reason I never worry about concatenating GFF files files together -- too often I am trying to reduce the size.