Hi Lieven,
Hope you're doing well. And no, I haven't (yet) hacked BOGAS again.
Please see below a bug report / complaint from Urmi, our bioinformatician currently annotating our Ectocarpus / Eurychasma RNAseq data.
Can you make your usual wonders?
Many thanks in advance,
Claire
PS for Urmi: I've seen your other messages (thanks!). All works fine and I'll get back to you as soon as I have a minute.
++++++++++++++++++++++++++++++++++++
Dr Claire GACHON
Principal Investigator in Molecular Phycology
Scottish Association for Marine Science
Scottish Marine Institute
PA37 1QA Oban
United Kingdom
claire.gachon(a)sams.ac.uk<mailto:claire.gachon@sams.ac.uk>
Skype contact : claire.gachon
Tel: 0044 16 31 559 318
Fax 0044 16 31 559 001
http://www.sams.ac.uk/claire-gachon
<http://www.sams.ac.uk/claire-gachon%0b>+++++++++++++++++++++++++++++++
From: Urmi Trivedi [mailto:urmi.trivedi@ed.ac.uk]<mailto:[mailto:urmi.trivedi@ed.ac.uk]>
Sent: 01 March 2013 13:49
To: Claire Gachon
Cc: gp3
Subject: Re: [Project 2012071] Analysis Update
Hi Claire,
As I said before, The GFF file downloaded from https://bioinformatics.psb.ugent.be/gdb/ectocarpus/ is not as per the current standard. The start position of a feature (exon, CDS, gene, etc) in some cases is larger than the end position, which is causing the software to break. Here are a few lines from the file for example
sctg_100 BOGAS exon 100155 99649 . - . ID=Esi0100_0021.1.15;Parent=Esi0100_0021.1;Ontology_term=SO:0000004
sctg_100 BOGAS three_prime_UTR 100155 99649 . - . ID=three_prime_UTR:Esi0100_0021.1.2;Parent=Esi0100_0021.1;Name=Esi0100_0021.1;Ontology_term=SO:0000205
sctg_100 BOGAS exon 322663 317617 . + . ID=Esi0100_0062.1.7;Parent=Esi0100_0062.1;Ontology_term=SO:0000004
sctg_100 BOGAS three_prime_UTR 322663 317617 . + . ID=three_prime_UTR:Esi0100_0062.1.5;Parent=Esi0100_0062.1;Name=Esi0100_0062.1;Ontology_term=SO:0000205
sctg_101 BOGAS exon 48870 48495 . + . ID=Esi0101_0012.1.3;Parent=Esi0101_0012.1;Ontology_term=SO:0000004
sctg_101 BOGAS three_prime_UTR 48870 48495 . + . ID=three_prime_UTR:Esi0101_0012.1.2;Parent=Esi0101_0012.1;Name=Esi0101_0012.1;Ontology_term=SO:0000205
sctg_17 BOGAS exon 514105 513859 . - . ID=Esi0017_0099.1.4;Parent=Esi0017_0099.1;Ontology_term=SO:0000004
sctg_17 BOGAS three_prime_UTR 514105 513859 . - . ID=three_prime_UTR:Esi0017_0099.1.2;Parent=Esi0017_0099.1;Name=Esi0017_0099.1;Ontology_term=SO:0000205
sctg_243 BOGAS exon 184367 183819 . + . ID=Esi0243_0025.1.4;Parent=Esi0243_0025.1;Ontology_term=SO:0000004
sctg_243 BOGAS three_prime_UTR 184367 183819 . + . ID=three_prime_UTR:Esi0243_0025.1.3;Parent=Esi0243_0025.1;Name=Esi0243_0025.1;Ontology_term=SO:0000205
There are 14 such entries in the file. This is causing the program to break. I think if you report this to annotation team, they may be able to fix this or explain the reason behind it. Or we might just have to proceed without these entries.
Best wishes,
Urmi
On 27/02/2013 13:52, Urmi Trivedi wrote:
Hi Claire,
I hope you had a good holiday.
As discussed last week, I have uploaded
1. raw reads for all samples
2. list of Euryunited contigs matching Ectocarpus after BLAST to nr at 1e-50 and
3. Counts generated for Euryunited-delta transcripts for Eurychasma infected samples.
at - http://genepool.bio.ed.ac.uk/seqdata/2012071_Gachon_Claire/
You can access the link above using your EASE friend username "claire.gachon(a)sams.ac.uk"<mailto:claire.gachon@sams.ac.uk> as login. Please let me know if you face any problems downloading the data or if you want me to give access to anyone else.
Alignments to Ectocarpus siliculosus genome is done. However, the GFF file (which contains annotation information) is not upto the standard that the software for counting reads per gene/transcript, expects. So, I will need to fix that. I am sorry but this will take a few more days. I will update you as soon as I have further results.
Best wishes,
Urmi
--
Urmi Trivedi
Lead Bioinformatician
The GenePool
Room 3.54, Ashworth Laboratories
Kings building's campus
University of Edinburgh
EH9 3JT, Edinburgh, UK.
Phone: +44 131 650 7403
Email: urmi.trivedi(a)ed.ac.uk<mailto:urmi.trivedi@ed.ac.uk>
--
Urmi Trivedi
Lead Bioinformatician
The GenePool
Room 3.54, Ashworth Laboratories
Kings building's campus
University of Edinburgh
EH9 3JT, Edinburgh, UK.
Phone: +44 131 650 7403
Email: urmi.trivedi(a)ed.ac.uk<mailto:urmi.trivedi@ed.ac.uk>
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