Moderator: pld

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pld4.4k
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Posts by pld

<prev • 650 results • page 1 of 65 • next >
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Comment: C: RNA Seq analysis of virally infected cells
... If you're working with a RNA virus, remember you'll have to find a way to differentiate between genome (and any genomic intermediates) and viral mRNA. ...
written 4 days ago by pld4.4k
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Comment: C: More than 300.000 peaks for a viral transcription factor - what could this mean?
... You said "expressed the TF", this would be in transfected cells, or were they infected with virus? Do you have a control in your RNA-Seq experiments (e.g. transfected for a non-TF EBV protein)? It would be important to know if the DEGs you've found are in response to the TF specifically and not in r ...
written 10 days ago by pld4.4k
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Comment: C: Softwares for Bacterial/Viral Classification from RNAseq
... Have you explored making a custom database for Kraken? ...
written 17 days ago by pld4.4k
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Comment: C: visualization problems: interesting research problems for postgraduate thesis [r
... I would personally love to see some better visualizations of transcriptome assembly quality. ...
written 24 days ago by pld4.4k
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Comment: C: Where does my RNASeq contamination fits on the Tree of Life?
... I'm a big fan of Kraken for screening against contamination, the program assigns a taxid to each read, with a little leg work you could filter off of that. If you use the kraken-translate tool you should be able to get the whole taxonomy for each read and filter there using keywords. E.g. get a list ...
written 27 days ago by pld4.4k
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Comment: C: Where does my RNASeq contamination fits on the Tree of Life?
... Why not start with filtering out reads that can be mapped to known bacterial/fungal species? ...
written 28 days ago by pld4.4k
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Comment: C: RNA-Seq And Genome Annotation file (GFF/GTF)
... Assuming Zika follows the canonical flavivirus replication cycle, a single mRNA will be generated (which lacks a poly-A tail). This mRNA will be translated into a single polyprotein precursor, which is then processed into individual viral proteins. I believe that the genome and mRNA are both positiv ...
written 28 days ago by pld4.4k
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Comment: C: In YOUR personal opinion, who are the top 5 bioinformatics researchers in NGS in
... 1-5: Me, obviously. ;) ...
written 6 weeks ago by pld4.4k
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Comment: C: Calling Qiime scripts sequencially in Python 2.7 program
... https://docs.python.org/2/library/subprocess.html Subprocess has what you want. Python can be rather clunky for this kind of thing. If you need data from some of these programs you're calling to end up being processed in python, it is better to pull the data into python from the "outside". You ma ...
written 9 weeks ago by pld4.4k
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Comment: C: Metagenome Next Generation Sequencing
... It really depends on what you're after and how much money you have to spend, I'd suggest reading some review articles. ...
written 9 weeks ago by pld4.4k

Latest awards to pld

Popular Question 1 day ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Appreciated 5 days ago, created a post with more than 5 votes. For C: Studying Bioinformatics - Reasons, motives and career
Popular Question 5 days ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Appreciated 9 days ago, created a post with more than 5 votes. For C: Studying Bioinformatics - Reasons, motives and career
Popular Question 11 days ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Popular Question 8 weeks ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Popular Question 12 weeks ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Scholar 3 months ago, created an answer that has been accepted. For A: difference between "predicted coding region" and "Hypothetical Protein
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Paper publication without qPCR validation
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Paper publication without qPCR validation
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Popular Question 5 months ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Paper publication without qPCR validation
Popular Question 8 months ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Appreciated 9 months ago, created a post with more than 5 votes. For C: Studying Bioinformatics - Reasons, motives and career
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Paper publication without qPCR validation
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Appreciated 9 months ago, created a post with more than 5 votes. For A: I want to re-open the old debate: python or perl ?
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Appreciated 9 months ago, created a post with more than 5 votes. For C: Studying Bioinformatics - Reasons, motives and career
Popular Question 9 months ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.

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