User: Buffo

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Buffo1.8k
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Posts by Buffo

<prev • 364 results • page 1 of 37 • next >
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Comment: C: Bray-Curtis dissimilarity for comparing genomes, how to normalize?
... 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 Buffo1.8k
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Bray-Curtis dissimilarity for comparing genomes, how to normalize?
... 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 ...
genome bray-curtis mummer sorensen normalization written 28 days ago by Buffo1.8k
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Star VS hisat2 for splicing reads
... 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 ...
rnaseq splicing star hisat2 written 4 months ago by Buffo1.8k
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Comment: A: PostDoc position at Human Genome Sequencing Center @ Baylor College of Medicine,
... Is this still open? Closing date? ...
written 8 months ago by Buffo1.8k
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Comment: C: Genome assembly with RNA-seq data?
... > 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 Buffo1.8k
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Comment: C: Genome assembly with RNA-seq data?
... 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 Buffo1.8k
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Answer: A: Genome assembly with RNA-seq data?
... 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 Buffo1.8k
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Comment: A: Postdocs @ New York City: Long Reads based Epigenomics, Metagenomics and Transcr
... Do not have institutional mail? ...
written 11 months ago by Buffo1.8k
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Answer: A: converting accession numbers to Gene Symbol
... [BioDBnet][1] is the most easy way :) [1]: https://biodbnet-abcc.ncifcrf.gov/ ...
written 12 months ago by Buffo1.8k
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Comment: C: Which is better: webgestalt vs david?
... 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 Buffo1.8k

Latest awards to Buffo

Popular Question 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, created a question with more than 1,000 views. For Genome assembly with RNA-seq data?
Popular Question 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 ?
Popular Question 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 ?
Appreciated 19 months ago, created a post with more than 5 votes. For A: Which is better: webgestalt vs david?
Scholar 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, created an answer with at least 3 up-votes. For A: How can I get FASTA if i have Names of proteins ?
Appreciated 19 months ago, created a post with more than 5 votes. For A: Which is better: webgestalt vs david?
Scholar 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, created an answer with at least 3 up-votes. For A: How can I get FASTA if i have Names of proteins ?
Popular Question 23 months ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Commentator 23 months ago, created a comment with at least 3 up-votes. For A: GO analysis of Soybean
Popular Question 23 months ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For A: GO analysis of Soybean
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Popular Question 2.2 years ago, created a question with more than 1,000 views. 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, created a question with more than 1,000 views. For piRNA target-interaction database?
Guru 2.5 years ago, received more than 100 upvotes.
Scholar 2.6 years ago, created an answer that has been accepted. For A: How can I get FASTA if i have Names of proteins ?

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