User: Buffo

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Buffo1.8k
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Posts by Buffo

<prev • 362 results • page 1 of 37 • next >
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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 7 weeks 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 6 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 7 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 7 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 7 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 8 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 9 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 9 months ago by Buffo1.8k
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Answer: A: Question about miRNAs
... No, 5p and 3p are different miRNAs, they come from the same precursor and are partially complementary in sequence but they may have completely different targets. Personally I recommend you not mix data from different databases, miRBase, mirpath from DianaTools and mirdeep2 works fine for me in hsa d ...
written 10 months ago by Buffo1.8k
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Comment: C: Detect synthetic miRNA via miRDeep2
... It is simply not possible, you need the precursor sequence. ...
written 10 months ago by Buffo1.8k

Latest awards to Buffo

Great Question 5 weeks ago, created a question with more than 5,000 views. For HISAT2 indexes, GRCm38 or mm10?
Popular Question 8 months ago, created a question with more than 1,000 views. For Genome assembly with RNA-seq data?
Popular Question 13 months ago, created a question with more than 1,000 views. For HISAT2 indexes, GRCm38 or mm10?
Teacher 13 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 14 months ago, created a question with more than 1,000 views. For piRNA target-interaction database?
Teacher 15 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 17 months ago, created a post with more than 5 votes. For A: Which is better: webgestalt vs david?
Scholar 17 months ago, created an answer that has been accepted. For A: How can I get FASTA if i have Names of proteins ?
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 17 months ago, created a post with more than 5 votes. For A: Which is better: webgestalt vs david?
Scholar 17 months ago, created an answer that has been accepted. For A: How can I get FASTA if i have Names of proteins ?
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 ?
Popular Question 20 months ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Commentator 20 months ago, created a comment with at least 3 up-votes. For A: GO analysis of Soybean
Popular Question 20 months ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Commentator 22 months ago, created a comment with at least 3 up-votes. For A: GO analysis of Soybean
Popular Question 22 months ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Popular Question 23 months ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Popular Question 24 months ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Popular Question 2.0 years ago, created a question with more than 1,000 views. For piRNA target-interaction database?
Popular Question 2.0 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?
Guru 2.3 years ago, received more than 100 upvotes.
Scholar 2.4 years ago, created an answer that has been accepted. For A: How can I get FASTA if i have Names of proteins ?
Teacher 2.4 years 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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