User: Buffo

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Buffo480
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Posts by Buffo

<prev • 150 results • page 1 of 15 • next >
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Comment: C: How to perform functional gene clustering?
... What about [ortoMCL][1], or [ortoMCL-DB][2]? [1]: https://wiki.hpcc.msu.edu/display/Bioinfo/OrthoMCL+Tutorial [2]: http://orthomcl.org/orthomcl/ ...
written 16 days ago by Buffo480
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Comment: C: classification of small RNA-seq
... Look at this [microRNA Sequencing Data Analysis Guideline][1] [1]: http://www.arraystar.com/reviews/microrna-sequencing-data-analysis-guideline/ ...
written 18 days ago by Buffo480
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Comment: C: miRNA analysis for de novo assembled RNA seq data
... You may try mapping validated miRNAs ([mirbase][1] for example) to your transcripts or to transcripts from mirgenes. But, in this case if RNA-seq library was not prepared as small-rnaseq library you can't find mature mirnas, short reads are not mirnas. [1]: http://www.mirbase.org/ftp.shtml ...
written 4 weeks ago by Buffo480
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Comment: C: miRNA family consevation plot
... [heatmap.2][1] en R :) [1]: http://sebastianraschka.com/Articles/heatmaps_in_r.html ...
written 4 weeks ago by Buffo480
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Comment: C: Retrieving coverage image
... look at this [How To Plot Read Coverage Over Many Different Genomic Regions?][1] [1]: https://www.biostars.org/p/62121/ ...
written 5 weeks ago by Buffo480
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Comment: C: Tumor Purity and miRNA / small RNA pipeline
... miRNA-seq data from small rna-seq library? If it is true, you can try Bowtie (v1) for alignment (recommended for short reads), for quality control try with [fastqc][1], it works for me. [1]: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ...
written 5 weeks ago by Buffo480
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Comment: C: Custom miRNA - target gene prediction by miRNA sequence
... I think this would help you [miRanda algorithm][1]. It works for me. [1]: http://cbio.mskcc.org/microrna_data/manual.html ...
written 7 weeks ago by Buffo480
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Comment: A: No differential gene expression after tuxedo protocol
... May be you want to read this: [Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown][1], actually tophat is obsolete software and kallisto I think is useful just for very curated genomes (and annotations). [1]: http://www.nature.com/nprot/journal/v11/n9/ ...
written 8 weeks ago by Buffo480
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Comment: C: RNA-seq gene expression normalization for independent samples
... What about Transcripts per million? (TPM), or RPKM? (Reads per kilobase per million)? ...
written 9 weeks ago by Buffo480
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Comment: C: miRNA analysis by miRDeep2
... As first approach I would recommend you doing by yourself, you can download mirna database from [mirdb][1], and then map your reads (each sample) to the database with [bowtie][2], after that you can count reads mapped to the mirDB with [samtools][3] idxstats or [htseq][4], normalize and found differ ...
written 10 weeks ago by Buffo480

Latest awards to Buffo

Supporter 10 weeks ago, voted at least 25 times.
Scholar 5 months ago, created an answer that has been accepted. For A: How can I get FASTA if i have Names of proteins ?
Centurion 6 months ago, created 100 posts.
Scholar 9 months ago, created an answer that has been accepted. For A: How can I get FASTA if i have Names of proteins ?
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 ?

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