Moderator: EagleEye

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EagleEye5.6k
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Investigating field of biology by applying logics of computer science, statistics and mathematics.

Posts by EagleEye

<prev • 872 results • page 1 of 88 • next >
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Comment: C: How do you convert featureCounts output into composition of mapped reads by RNA
... Consider this matrix as 'featurecounts.matrix' in the below example. Follow other steps I mentioned. ...
written 5 days ago by EagleEye5.6k
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Comment: C: Mapsplice 2 error
... Please report your recent command used and also the error log. ...
written 11 days ago by EagleEye5.6k
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Comment: C: GSEA analysis and pathway mapping
... https://www.biostars.org/p/108669/ ...
written 13 days ago by EagleEye5.6k
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Comment: C: How do you convert featureCounts output into composition of mapped reads by RNA
... You mean you got matrix like this, Geneid Ctrl Treated ENSG00000223972 0 0 ENSG00000227232 0 0 ENSG00000278267 0 0 ...
written 13 days ago by EagleEye5.6k
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Answer: A: How do you convert featureCounts output into composition of mapped reads by RNA
... If in case you used GTF file as reference annotation, 1) You can just convert the annotation into table format. Example: https://www.biostars.org/p/208102/#212022 2) Import you GTF converted table (`Geneid GeneSymbol Chromosome Start End Class Strand Length`) and your matrix from featurecounts (` ...
written 13 days ago by EagleEye5.6k
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Answer: A: Regarding cancer data analysis
... https://www.biostars.org/p/108669/ With this tool you can retrieve all pathways with corresponding genes for your desired organism as simple text/table format. [Example usage here][1] [1]: https://www.biostars.org/p/197414/#197416 ...
written 13 days ago by EagleEye5.6k
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Answer: A: Mapsplice 2 error
... Instead of `-c bowtie2index.fa` you need to provide the directory path where the 'bowtie2index.fa' is stored. If it is in current directory, you can just specify `'-c ./'`. [MapSplice user guide.][1] [1]: http://www.netlab.uky.edu/p/bioinfo/MapSpliceManual ...
written 13 days ago by EagleEye5.6k
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Answer: A: Human and animal (mouse) expression datasets for the same tissues
... Mouse (Mus musculus) RNA-seq from [ENCODE][1]. You have two replicates per tissue samples (heart and liver). Human RNA-seq from [ENCODE][2] for same tissues such as heart and liver. [1]: https://www.encodeproject.org/matrix/?type=Experiment&assay_title=total+RNA-seq&biosample_type=tissu ...
written 16 days ago by EagleEye5.6k
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Answer: A: How to integrate GTEx data for variant annotation to understand the tissue speci
... These articles will give you some idea to proceed with your analysis. [Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation][1] [eQTL mapping identifies insertion- and deletion-specific eQTLs in multiple tissues][2] [Genetic effects o ...
written 18 days ago by EagleEye5.6k
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Comment: C: circRNA database of TCGA
... Sorry I do not have much idea on circRNAs from TCGA. ...
written 20 days ago by EagleEye5.6k

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