User: Buffo

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Buffo1.8k
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Posts by Buffo

<prev • 361 results • page 1 of 37 • next >
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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 weeks 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 3 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 3 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 3 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 4 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 5 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 5 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 6 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 6 months ago by Buffo1.8k
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Comment: C: *.rnk file preparation for GSEA analysis
... Filter by FDR looks good for me, however filtering by an arbitrary FC may be a source of bias. I usually filter by FDR, and use the complete matrix (log2fold as rank). Ranked list for Webgestalt is a two column list, gene and rank (logfold). ...
written 6 months ago by Buffo1.8k

Latest awards to Buffo

Popular Question 3 months ago, created a question with more than 1,000 views. For Genome assembly with RNA-seq data?
Popular Question 8 months ago, created a question with more than 1,000 views. For HISAT2 indexes, GRCm38 or mm10?
Teacher 9 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 10 months ago, created a question with more than 1,000 views. For piRNA target-interaction database?
Teacher 10 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 12 months ago, created a post with more than 5 votes. For A: Which is better: webgestalt vs david?
Scholar 12 months ago, created an answer that has been accepted. For A: How can I get FASTA if i have Names of proteins ?
Teacher 12 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 12 months ago, created a post with more than 5 votes. For A: Which is better: webgestalt vs david?
Scholar 12 months ago, created an answer that has been accepted. For A: How can I get FASTA if i have Names of proteins ?
Teacher 12 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 16 months ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Commentator 16 months ago, created a comment with at least 3 up-votes. For A: GO analysis of Soybean
Popular Question 16 months ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Commentator 18 months ago, created a comment with at least 3 up-votes. For A: GO analysis of Soybean
Popular Question 18 months ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Popular Question 19 months ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Popular Question 19 months ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Popular Question 20 months ago, created a question with more than 1,000 views. For piRNA target-interaction database?
Popular Question 20 months ago, created a question with more than 1,000 views. For piRNA target-interaction database?
Popular Question 21 months ago, created a question with more than 1,000 views. For piRNA target-interaction database?
Guru 23 months ago, received more than 100 upvotes.
Scholar 2.0 years ago, created an answer that has been accepted. For A: How can I get FASTA if i have Names of proteins ?
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: How can I get FASTA if i have Names of proteins ?
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: How to convert GTF to gff file for read count using HTSeq

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