Hi Binu,
It's a bit hard to really diagnose the problem without access to the
whole files. Perhaps you can create a tarball or zip them up
(as they're text, they should compress pretty well) and try to e-mail
the compressed file as an attachment or host them somewhere so that
I can download them.
Quickly glancing at the GFF3 file generated, I've noticed that there
are no "match" objects for the "match_part" ones. I'm curious whether
the "match" objects exist but just didn't happen to make it in the
pasted data? Or is it missing in the whole file?
Cheers,
Ed
On Thu, 18 Feb 2010, Binu George wrote:
Hi Ed,
Thanks for your response!
<quote>Did you convert the BLAT output to GFF or GFF3 format? </quote>
Yeah, we did (using the script available at
http://iubio.bio.indiana.edu/gmod/tandy/blat2gff.pl)
The files are *huge*. Hence added here are excerpts from the three files.
1. BLAT results
------------------------------------------------------------------
42 3 0 0 0 0 0 0 +
HWUSI-EAS1599_1:6:1:4:1768 75 0 45
PdactyK2.0Scaffold_1529741_length_19394 19394 1903 1948 1 45,
0, 1903,
43 2 0 0 0 0 0 0 +
HWUSI-EAS1599_1:6:1:4:1783 75 0 45
PdactyK2.0Scaffold_1525681_length_26055 26055 5512 5557 1 45,
0, 5512,
39 1 0 0 0 0 0 0 -
HWUSI-EAS1599_1:6:1:4:1905 75 0 40
PdactyK2.0Scaffold_1429791_length_34476 34476 8554 8594 1 40,
35, 8554,
74 1 0 0 0 0 0 0 +
HWUSI-EAS1599_1:6:1:4:1697 75 0 75
PdactyK2.0Scaffold_1407171_length_9181 9181 6781 6856 1 75,
0, 6781,
73 2 0 0 0 0 0 0 -
HWUSI-EAS1599_1:6:1:5:1568 75 0 75
PdactyK2.0Scaffold_1352831_length_28486 28486 8073 8148 1 75,
0, 8073,
56 4 0 0 0 0 1 86 -
HWUSI-EAS1599_1:6:1:5:1116 75 15 75
PdactyK2.0Scaffold_1431621_length_2994 2994 351 497 2
25,35, 0,25, 351,462,
34 3 0 0 0 0 0 0 -
HWUSI-EAS1599_1:6:1:5:1116 75 15 52
PdactyK2.0Scaffold_1339081_length_142003 142003 79814 79851 1
37, 23, 79814,
73 2 0 0 0 0 0 0 -
HWUSI-EAS1599_1:6:1:5:1223 75 0 75
PdactyK2.0Scaffold_1525681_length_26055 26055 5575 5650 1 75,
0, 5575,
------------------------------------------------------------------
2. GBK file
------------------------------------------------------------------
LOCUS HWUSI-EAS1599_1:6:1:3:1506 75 bp dna linear
UNK
DEFINITION 1 0
ACCESSION unknown
FEATURES Location/Qualifiers
ORIGIN
1 gaatatgtgg agacaaagat ccctgcgata cacaagaaat aatctatagg aattcatgaa
61 aacaagagat atcct
//
LOCUS HWUSI-EAS1599_1:6:1:3:1742 75 bp dna linear
UNK
DEFINITION 2 0
ACCESSION unknown
FEATURES Location/Qualifiers
ORIGIN
1 aatgaagcaa aggtacgtga ctgagataga caaggcaaaa gaagtataca gacaagtaat
61 aagaatatga gagcc
//
LOCUS HWUSI-EAS1599_1:6:1:4:1768 75 bp dna linear
UNK
DEFINITION 3 0
ACCESSION unknown
FEATURES Location/Qualifiers
ORIGIN
1 cggtgcttag aaccagggtg ttcgtgcaaa aaataagaag ccatgacact gaccgaccat
61 aataagaggg gagtg
//
------------------------------------------------------------------
3. GFF file
------------------------------------------------------------------
PdactyK2.0Scaffold_1529741_length_19394 BLAT match_part 1904 1948
56.00 + .
Parent=HWUSI-EAS1599_1:6:1:4:1768_mid1;Target=HWUSI-EAS1599_1:6:1:4:1768 1 45
PdactyK2.0Scaffold_1525681_length_26055 BLAT match_part 5513 5557
57.33 + .
Parent=HWUSI-EAS1599_1:6:1:4:1783_mid1;Target=HWUSI-EAS1599_1:6:1:4:1783 1 45
PdactyK2.0Scaffold_1429791_length_34476 BLAT match_part 8555 8594
52.00 - .
Parent=HWUSI-EAS1599_1:6:1:4:1905_mid1;Target=HWUSI-EAS1599_1:6:1:4:1905 75
36
PdactyK2.0Scaffold_1407171_length_9181 BLAT match_part 6782 6856
98.67 + .
Parent=HWUSI-EAS1599_1:6:1:4:1697_mid1;Target=HWUSI-EAS1599_1:6:1:4:1697 1 75
PdactyK2.0Scaffold_1352831_length_28486 BLAT match_part 8074 8148
97.33 - .
Parent=HWUSI-EAS1599_1:6:1:5:1568_mid1;Target=HWUSI-EAS1599_1:6:1:5:1568 75 1
------------------------------------------------------------------
Thanks again!
--Binu
On 17 Feb 2010, at 23:25, Ed Lee wrote:
Hi Binu,
It is possible that the BLAT format has changed and broken the adapter.
I could take a look at the file if you forward the BLAT results
along with the GBK and GFF3 files.
Did you convert the BLAT output to GFF or GFF3 format? The GFF
format supported in Apollo is one used by the Ensembl folks, so it
might not work with data generated elsewhere. You really want to
use the GFF3 format. If it is in GFF3 format, I could take a
look at the generated file and see what might have gone wrong.
Cheers,
Ed
On Tue, 9 Feb 2010, Binu George wrote:
Hi,
I am new to using the Apollo genome browser, and am having some trouble
trying to overlap BLAT result output with my sequence information.
We have genbank and gff file containing the genomic sequence of a contig
from a genome. I am able to use apollo to view this data along with all
the annotations.
Along with that, we have the result of a BLAT run of mRNA sequences
matched
against this genbank file (in .psl format). We are trying to overlay the
BLAT result over the currently view contig data, but are unable to do so.
On trying to open the '.psl' file, we get this error logged in the
'stdout.log'
file
-----------
ERROR: Failed to parse blat data
-----------
We converted the .psl to gff format. But on trying to load this gff file
doesn't work either. The popped up dialog box freezes, and there is no
corresponding message logged in the stdout/stderr log files.
Any help in this regard is appreciated!
Thanks!
--Binu
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