User: Buffo

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Buffo1.1k
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Posts by Buffo

<prev • 242 results • page 1 of 25 • next >
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Comment: C: Aligning miRNA reads to miRbase
... I recommend you to use both, mature and hairpin because you may found new miRNA variants or "isoforms". And also, recommend you to use bowtie (no bowtie2 or blast) to align them, it is easy to handle and filter multihits. ...
written 5 hours ago by Buffo1.1k
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Comment: C: Hide insertion sites in IGV Browser, is it possible?
... Thanks Pierre :D, exactly what I cant see in front my eyes. ...
written 3 days ago by Buffo1.1k
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Hide insertion sites in IGV Browser, is it possible?
... Hi, By default IGV indicates insertions with respect to the reference with a purple I, and I would like to hide it or change the color, I have read the manual and it is making me crazy, I can´t find the way to do it, somebody knows if it is possible? ...
alignment igv written 3 days ago by Buffo1.1k
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Answer: A: Up-to-date RNA-Seq Analysis Training/Courses/Papers
... The [article][1] of the new tuxedo protocol :) [1]: https://www.nature.com/articles/nprot.2016.095.pdf ...
written 5 days ago by Buffo1.1k
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Comment: C: RNAseq analysis with very close species
... Yes exactly as Carlo asked, option 2 depends on how close-related genomes are, probably comparing % of aligned reads? (excluding multihit), but also option 1 would works after a genome refinement (filter redundant scaffolds, low coverage, etc.). ...
written 5 days ago by Buffo1.1k
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Comment: C: RNAseq analysis with very close species
... What about performing de novo transcriptomic assembly for the specie with fragmented genome? [rnaspades][1] works fine form me. [1]: http://cab.spbu.ru/software/rnaspades/ ...
written 5 days ago by Buffo1.1k
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Comment: C: Triangle heatmap with heatmap.2
... Something like a [corrplot][1]? [1]: https://cran.r-project.org/web/packages/corrplot/vignettes/corrplot-intro.html ...
written 7 days ago by Buffo1.1k
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Comment: C: What is the purpose of having reference genome of other species during miRDeep2?
... Probably because most of the mature miRNAs described to date, are conserved sequences. One condition to filter probable miRNAs to other short non-codings RNAs is if they (or closely related short sequences) have been described to show some inhibitor activity. ...
written 9 days ago by Buffo1.1k
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Answer: A: Options for long-read diploid assembly
... Probably [CLC Genomics Workbench][1] and [HGAP][2] are the best choices for long leads. [1]: https://www.qiagenbioinformatics.com/products/clc-genomics-workbench/ [2]: https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/HGAP ...
written 24 days ago by Buffo1.1k
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Comment: C: Suggestions for better and accurate tool for PanGenome analysis.
... Something like [CD-HIT][1] and then parse the output? probably it would works as first insigth to what you want to do, however I think this is a complicated job even for closely-related species, so, for multiple genera... please tell me if you find another suitable solution. [1]: http://weizhong ...
written 5 weeks ago by Buffo1.1k

Latest awards to Buffo

Popular Question 24 days ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Pipeline for genome annotation?
Popular Question 6 weeks ago, created a question with more than 1,000 views. For piRNA target-interaction database?
Popular Question 6 weeks ago, created a question with more than 1,000 views. For piRNA target-interaction database?
Popular Question 3 months ago, created a question with more than 1,000 views. For piRNA target-interaction database?
Guru 5 months ago, received more than 100 upvotes.
Scholar 6 months ago, created an answer that has been accepted. For A: How can I get FASTA if i have Names of proteins ?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How can I get FASTA if i have Names of proteins ?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to convert GTF to gff file for read count using HTSeq
Scholar 6 months ago, created an answer that has been accepted. For A: How can I get FASTA if i have Names of proteins ?
Teacher 6 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 9 months ago, created a question with more than 1,000 views. For Genomic assembly with spades
Supporter 13 months ago, voted at least 25 times.
Scholar 17 months ago, created an answer that has been accepted. For A: How can I get FASTA if i have Names of proteins ?
Centurion 17 months ago, created 100 posts.
Scholar 20 months ago, created an answer that has been accepted. For A: How can I get FASTA if i have Names of proteins ?
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 ?

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