User: Buffo
Buffo • 1.8k
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Posts by Buffo
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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 28 days ago by
Buffo • 1.8k
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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 28 days 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 4 months ago by
Buffo • 1.8k
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872
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... Is this still open? Closing date? ...
written 8 months ago by
Buffo • 1.8k
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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 10 months ago by
Buffo • 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 10 months ago by
Buffo • 1.8k
1
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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 10 months ago by
Buffo • 1.8k
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468
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... Do not have institutional mail? ...
written 11 months ago by
Buffo • 1.8k
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315
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... [BioDBnet][1] is the most easy way :)
[1]: https://biodbnet-abcc.ncifcrf.gov/ ...
written 12 months ago by
Buffo • 1.8k
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... I am not sure if is faster but agree with "nice plots", however, it does not use a ranked list as WebGestalt. In my opinion it is a very important advantage for most uses. ...
written 12 months ago by
Buffo • 1.8k
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3 months ago,
created a question with more than 1,000 views.
For piRNA target-interaction database?
Great Question
4 months ago,
created a question with more than 5,000 views.
For HISAT2 indexes, GRCm38 or mm10?
Popular Question
10 months ago,
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For Genome assembly with RNA-seq data?
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15 months ago,
created a question with more than 1,000 views.
For HISAT2 indexes, GRCm38 or mm10?
Teacher
16 months ago,
created an answer with at least 3 up-votes.
For A: How can I get FASTA if i have Names of proteins ?
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17 months ago,
created a question with more than 1,000 views.
For piRNA target-interaction database?
Teacher
17 months ago,
created an answer with at least 3 up-votes.
For A: How can I get FASTA if i have Names of proteins ?
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19 months ago,
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For A: Which is better: webgestalt vs david?
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For A: How can I get FASTA if i have Names of proteins ?
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19 months ago,
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For A: How can I get FASTA if i have Names of proteins ?
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19 months ago,
created a post with more than 5 votes.
For A: Which is better: webgestalt vs david?
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19 months ago,
created an answer that has been accepted.
For A: How can I get FASTA if i have Names of proteins ?
Teacher
19 months ago,
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For A: How can I get FASTA if i have Names of proteins ?
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For Pipeline for genome annotation?
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23 months ago,
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2.1 years ago,
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For A: GO analysis of Soybean
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2.1 years ago,
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For Pipeline for genome annotation?
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2.2 years ago,
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For Pipeline for genome annotation?
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For piRNA target-interaction database?
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For piRNA target-interaction database?
Popular Question
2.4 years ago,
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For piRNA target-interaction database?
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2.5 years ago,
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2.6 years ago,
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For A: How can I get FASTA if i have Names of proteins ?
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