User: enxxx23
enxxx23 • 230
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Posts by enxxx23
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... One way to do get more information about a fusion transcript found only by one tool would be to google (or search pubmed or google scholar?) the fusion gene and see where that fusion has been reported previously and in what type of cancers. If that fusion has been published previously in articles/da ...
written 6 weeks ago by
enxxx23 • 230
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... Different tools use different versions/sources of gene annotations and different genome releases/patches (eg. hg18/hg19). Therefore, as one would expect, one gets different results. I would say the the differences in Venn diagram can be explained mostly by differences in gene annotations uses (e.g. ...
written 6 weeks ago by
enxxx23 • 230
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... It looks like CPM is computed here.
TPM for a gene should be computed using the TPMs computed from transcripts.
It looks like a big confusion is going on regarding CPM, TPM for genes, and TPM for transcripts. ...
written 10 weeks ago by
enxxx23 • 230
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... True, I should have mentioned the target organisms, which in this case are eukaryotes.
Retroviruses do not have RNA so doing RNA-seq on retroviruses is the only choice! ;-) ...
written 4 months ago by
enxxx23 • 230
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... BWA MEM is not a RNA-seq aligner by design. ...
written 4 months ago by
enxxx23 • 230
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9 follow
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... What is the fastest (non-pseudo) aligner for RNA-seq illumina seq data today in year 2019?
...
written 4 months ago by
enxxx23 • 230
• updated
4 months ago by
kristoffer.vittingseerup • 2.0k
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... I totally agree! Do not use TopHat(2)! ...
written 7 months ago by
enxxx23 • 230
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... It would be great to have more info here, like for example:
- number of replicates,
- info about the times points (e.g. before and after the treatment time points?)
- type of disease: cancer or non-cancer
- tissues of origin for the samples (are all from the same tissue?),
- is there healthy tissue ...
written 7 months ago by
enxxx23 • 230
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Comment:
C: Best tool for variant calling
... I concurr. This is my experience too.
What version of samtools are you using? ...
written 7 months ago by
enxxx23 • 230
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... FusionCatcher
https://sourceforge.net/projects/fusioncatcher/ ...
written 8 months ago by
enxxx23 • 230
Latest awards to enxxx23
Popular Question
15 months ago,
created a question with more than 1,000 views.
For Public RNA-seq dataset for human & 2x250bp or longer
Teacher
4.2 years ago,
created an answer with at least 3 up-votes.
For A: The new era of bioinformatics: simple and fast tools, fewer and more informative
Commentator
4.6 years ago,
created a comment with at least 3 up-votes.
For C: Genomics is not Special. Computational Biologists are reinventing the wheel for
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