User: User 4014

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User 401420
Reputation:
20
Status:
New User
Location:
Sweden
Last seen:
1 month ago
Joined:
7 years, 2 months ago
Email:
c**********@ymail.com

Posts by User 4014

<prev • 34 results • page 1 of 4 • next >
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Comment: C: EMBL-api-validator -- WARNING: "exon" usually expected to be at least "15" nt lo
... I will carefully examine those models with short exon and will keep bad ones out of the annotation. But for those with proper/reasonable blastp hits, I will use the script to correct them. :) ...
written 4 weeks ago by User 401420
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Comment: C: EMBL-api-validator -- WARNING: "exon" usually expected to be at least "15" nt lo
... Thanks again Juke! :) ...
written 4 weeks ago by User 401420
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Comment: C: EMBL-api-validator -- WARNING: "exon" usually expected to be at least "15" nt lo
... Good to hear that you also experienced similar problem. The script would be fantastic. May you share me the script, please? Thanks in advance! ...
written 4 weeks ago by User 401420
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Comment: C: EMBL-api-validator -- WARNING: "exon" usually expected to be at least "15" nt lo
... Yes, I did nucmer to remove repetitive contigs <500 bp before feeding the genome to FUNGAP, but I did not look at the BUSCO results though since I thought FUNGAP would sieve out those small and highly fragmented models. There is a genome of close relatives. I think the plan is .. I will take a ...
written 4 weeks ago by User 401420
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Comment: C: EMBL-api-validator -- WARNING: "exon" usually expected to be at least "15" nt lo
... The pipeline does blastp/interproscan/blastn/BUSCO before choosing the best models. So I thought it is sufficient. Plus I don't really know how to check the models. May you suggest? ...
written 4 weeks ago by User 401420
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Comment: C: EMBL-api-validator -- WARNING: "exon" usually expected to be at least "15" nt lo
... The identity between the two proteins is only 36% and they are much different in sizes (63 aa vs 1118 aa). Actually it is not only one model that got the problem. Took some more for blastp and they seem correct with nice alignment to other proteins, but still contain a tiny tail of 2-3 aa at the end ...
written 4 weeks ago by User 401420
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Comment: C: EMBL-api-validator -- WARNING: "exon" usually expected to be at least "15" nt lo
... I did blastp and the only match is a response regulator (1118 aa) from a bacterium Maricaulis salignorans. I should have done blastp, not only interproscan. Perhaps it's better to remove this predicted protein? ...
written 4 weeks ago by User 401420
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Comment: C: EMBL-api-validator -- WARNING: "exon" usually expected to be at least "15" nt lo
... Hmm..it seems like so. One of the three exons (last one) is only 6 bases. The predicted protein itself is 63 aa though. Do you have a suggestion how should I treat this exon and the corresponding protein? It is a draft genome, assembled with Spades 3.10 and annotated using FUNGAP (https://github.com ...
written 4 weeks ago by User 401420
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EMBL-api-validator -- WARNING: "exon" usually expected to be at least "15" nt long.
... Hi folks, I am preparing a flat file of a fungal genome for submission to EMBL. I used EMBL-API_validator-1.1.263 to check the flat file and got warnings "WARNING: "exon" usually expected to be at least "15" nt long. Please check the accuracy. ". May you please advise how to fix it? Or should I ju ...
genome embl submission written 4 weeks ago by User 401420 • updated 4 weeks ago by Juke-341.8k
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Comment: C: Please advice on an experiment set-up for RNA-Seq
... Thanks for your suggestions. I will increase the replication to three. However, I was wondering what about using each individual for both treatment and control since I expect each individual will have at least 5 twigs. I can then use only 6 individuals from each tree genotype per each fungal genotyp ...
written 10 months ago by User 401420

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