User: Buffo
Buffo • 480
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Posts by Buffo
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... 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
Buffo • 480
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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
Buffo • 480
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... 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
Buffo • 480
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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
Buffo • 480
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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
Buffo • 480
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... 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
Buffo • 480
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... 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
Buffo • 480
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... 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[Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown][1], actually tophat is obsolete software and kallisto I think is useful just for very curated genomes (and annotations).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
Buffo • 480
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... What about Transcripts per million? (TPM), or RPKM? (Reads per kilobase per million)? ...
written 9 weeks ago by
Buffo • 480
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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
Buffo • 480
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