User: Buffo
Buffo • 1.8k
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Posts by Buffo
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... Hi,
I have installed orthoMCL using conda, anybody knows how to set/get login and password (of mysql)? ...
written 3 months ago by
Buffo • 1.8k
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... FastANI is faster than others programs such as Nucmer but it has a few disadvantages such as:
.- Is not recommended for fragmented or short genomes (N50 be ≥10 Kbp).
.- No ANI output is reported for a genome pair if ANI value is much below 80%.
But in my case would be a good alternative. T ...
written 4 months ago by
Buffo • 1.8k
2
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... Hi everyone,
I am comparing whole genomes of a closely related species using Nucmer. I want to calculate the %of similarity based on the bases aligned from each genome using Bray-Curtis dissimilarity (I had also tried Sorensen coefficient). The problem is that some genomes have very different genom ...
written 4 months ago by
Buffo • 1.8k
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... Hi everyone,
I performed a splicing analysis using hisat2 as a mapper, everything goes perfect, as expected. But, by using STAR I am not able to find any splicing event (splice junctions). I am using default parameters in both cases and obviously the same data. I am very familiar using hisat2 but n ...
written 8 months ago by
Buffo • 1.8k
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1.0k
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... Is this still open? Closing date? ...
written 13 months ago by
Buffo • 1.8k
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2
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1.8k
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... > Moreover: Pilon should be used with DNA-seq reads, not RNAseq reads!
Why not? If you move from hsa or mm there are lot of eucaryotes without splicing events (Just keep that in mind), in all those cases is validto use Pilon. Have you ever used Pilon?
Before using pilon I tried at least 5 or 6 ...
written 14 months ago by
Buffo • 1.8k
1
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2
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1.8k
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... From Pilon;
> Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including:
> Single base differences
> Small indels
> Larger indel or block s ...
written 14 months ago by
Buffo • 1.8k
1
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2
answers
1.8k
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... I had forgotten this question, finally I used [Pilon][1] for polishing my draft assembly using paired-end RNA-seq sequences. It works very well for me.
[1]: https://github.com/broadinstitute/pilon/wiki ...
written 14 months ago by
Buffo • 1.8k
0
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0
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550
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... Do not have institutional mail? ...
written 15 months ago by
Buffo • 1.8k
1
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1
answer
598
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1
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... [BioDBnet][1] is the most easy way :)
[1]: https://biodbnet-abcc.ncifcrf.gov/ ...
written 16 months ago by
Buffo • 1.8k
Latest awards to Buffo
Popular Question
4 months ago,
created a question with more than 1,000 views.
For piRNA target-interaction database?
Popular Question
7 months ago,
created a question with more than 1,000 views.
For piRNA target-interaction database?
Great Question
8 months ago,
created a question with more than 5,000 views.
For HISAT2 indexes, GRCm38 or mm10?
Popular Question
14 months ago,
created a question with more than 1,000 views.
For Genome assembly with RNA-seq data?
Popular Question
19 months ago,
created a question with more than 1,000 views.
For HISAT2 indexes, GRCm38 or mm10?
Teacher
20 months ago,
created an answer with at least 3 up-votes.
For A: How can I get FASTA if i have Names of proteins ?
Popular Question
21 months ago,
created a question with more than 1,000 views.
For piRNA target-interaction database?
Teacher
21 months ago,
created an answer with at least 3 up-votes.
For A: How can I get FASTA if i have Names of proteins ?
Appreciated
23 months ago,
created a post with more than 5 votes.
For A: Which is better: webgestalt vs david?
Scholar
23 months ago,
created an answer that has been accepted.
For A: How can I get FASTA if i have Names of proteins ?
Teacher
23 months ago,
created an answer with at least 3 up-votes.
For A: How can I get FASTA if i have Names of proteins ?
Appreciated
23 months ago,
created a post with more than 5 votes.
For A: Which is better: webgestalt vs david?
Scholar
23 months ago,
created an answer that has been accepted.
For A: How can I get FASTA if i have Names of proteins ?
Teacher
23 months ago,
created an answer with at least 3 up-votes.
For A: How can I get FASTA if i have Names of proteins ?
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For Pipeline for genome annotation?
Commentator
2.2 years ago,
created a comment with at least 3 up-votes.
For A: GO analysis of Soybean
Popular Question
2.3 years ago,
created a question with more than 1,000 views.
For Pipeline for genome annotation?
Commentator
2.4 years ago,
created a comment with at least 3 up-votes.
For A: GO analysis of Soybean
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For Pipeline for genome annotation?
Popular Question
2.5 years ago,
created a question with more than 1,000 views.
For Pipeline for genome annotation?
Popular Question
2.5 years ago,
created a question with more than 1,000 views.
For Pipeline for genome annotation?
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For piRNA target-interaction database?
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For piRNA target-interaction database?
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For piRNA target-interaction database?
Guru
2.9 years ago,
received more than 100 upvotes.
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