Hello Gundala,
I can't speak to how ENSEMBL creates their MAF files. Your question
may be
better suited for their list. That said, I will share with you some of my
observations.
From the MAF snippet you provide below, I see that it differs from our
MAF
files in at least one way. When we create a MAF file, we typically include the
name of the organisms to/from which we are aligning. Like so:
##maf version=1 scoring=autoMZ.v1
a score=47131.000000
s dm3.chrYHet 0 159 + 347038 AGGGTCAC [cut here]
s droSec1.super_438 3565 163 - 11586 --ggtccttga [cut here]
Note that before the "."chromName, we list the organism name. I see
that the
ENSEMBL MAF does not have the organism name listed. It's possible that the
mafToAxt program is expecting to find that organism name.
You can read more about the UCSC MAF file type here:
http://genome.ucsc.edu/FAQ/FAQformat#format5
Regards,
----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
Please feel free to search the Genome mailing list archives by visiting our
home
page, clicking on "Contact Us", then typing a word or phrase into the search
box. On that same page
(http://genome.ucsc.edu/contacts.html), you can subscribe to the Genome mailing
list.
Gundala Viswanath wrote:
> Dear all,
>
> Can we use mafToAxt on maf file aligned on genome downloaded
> from ENSEMBL?
>
> Example below is the alignment of D. Melanogaster versus A. Aegypti
> downloaded from: http://www.ensembl.org/info/data/ftp/index.html
>
> a score=50
> s 3L 12244269 106 + 31566707 ATGATCGATAAAAAT [cut here]
> s supercont1.1440 2899257 111 - 49087461 ATAATGTATATAAAT [cut here]
> ..etc...
> a score=51
> s X 29357053 58 + 31566707 TTTGCAAAAAAAAAAAAAAAa [cut here]
> s supercont1.1292 44393263 59 - 49087461 TTTGCAAAAAAAAAAAAAAAAT [cut here]
> ..etc...
>
> In particular I have problem passing the "tname" an "qName" parameter.
>
> $ mafToAxt
> mafToAxt - Convert from maf to axt format
> usage:
> mafToAxt in.maf tName qName output
>
>
> - Gundala Viswanath
> Jakarta - Indonesia
> _______________________________________________
> Genome maillist - [email protected]
> http://www.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
http://www.soe.ucsc.edu/mailman/listinfo/genome
