Moderator: EagleEye
EagleEye ♦ 5.6k
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Investigating field of biology by applying logics of computer science, statistics and mathematics.
Posts by EagleEye
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... Consider this matrix as 'featurecounts.matrix' in the below example. Follow other steps I mentioned. ...
written 5 days ago by
EagleEye ♦ 5.6k
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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
EagleEye ♦ 5.6k
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Comment:
C: GSEA analysis and pathway mapping
... https://www.biostars.org/p/108669/ ...
written 13 days ago by
EagleEye ♦ 5.6k
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... You mean you got matrix like this,
Geneid Ctrl Treated
ENSG00000223972 0 0
ENSG00000227232 0 0
ENSG00000278267 0 0
...
written 13 days ago by
EagleEye ♦ 5.6k
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... 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
EagleEye ♦ 5.6k
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... 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
EagleEye ♦ 5.6k
0
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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
EagleEye ♦ 5.6k
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... 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
EagleEye ♦ 5.6k
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... 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
EagleEye ♦ 5.6k
0
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1
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121
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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
EagleEye ♦ 5.6k
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