Moderator: Friederike

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Friederike5.2k
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Genomic Scientist @ Weill Cornell Medical College (Applied Bioinformatics Core)

http://abc.med.cornell.edu/

Posts by Friederike

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Comment: C: R error: vector memory exhausted
... Don't you want `#NA / all` <= 0.05 then? ...
written 9 weeks ago by Friederike5.2k
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Comment: C: R error: vector memory exhausted
... in addition, you may want to check out the [vcftools suite](http://vcftools.sourceforge.net/), they may already provide a function that does exactly what you want. ...
written 9 weeks ago by Friederike5.2k
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Answer: A: R error: vector memory exhausted
... I wouldn't use R for the filtering because the default working philosophy of R is to load everything into memory *before* doing anything to a given object. I'd probably try to filter before reading into R, e.g. using standard command line tools: ``` $ cat test.txt Sample_1 Sample_2 Sample_3 ...
written 9 weeks ago by Friederike5.2k
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Comment: C: List of plant long read genome assemblies
... Where have you looked so far? ...
written 9 weeks ago by Friederike5.2k
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Comment: C: How to define a column containing gene names "text" (instead of "general") when
... Because they're not scared of altering XLS files. Anyway, as I detailed above, I'm somewhat ok with that, but, on the other hand, this behavior tells me that the format type of the gene name column is not correctly assigned by either package. Just something to be aware of. ...
written 10 weeks ago by Friederike5.2k
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Comment: C: How to define a column containing gene names "text" (instead of "general") when
... Thanks for sharing! That behavior is consistent with the `openxlsx` solution described above, too. Now the question is: what happens when you open your `test.xlsx` file with Excel and *add* another entry (e.g. Sept11) in the gene name column? ...
written 10 weeks ago by Friederike5.2k
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Comment: C: Converting and sorting .sam at the same time
... What did the log file of STAR have to say about the error? If you want to actually solve issues rather than just trying out new tools you might be unfamiliar with, it might be more useful to try to follow the suggestions by the users here. ...
written 10 weeks ago by Friederike5.2k
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Comment: C: How I know a file is sam or bam, sorted or unsorted
... Just to follow up on Arup's advice -- given that you seem to have generated a SAM file instead of a BAM file, it seems highly likely that the conversion and sorting failed [EDIT:], therefore it would be highly advisable to understand what caused STAR to not honor your parameter choices, i.e. read th ...
written 10 weeks ago by Friederike5.2k
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Answer: A: Putting R codes on MS word document
... RStudio also supports the generation of Word documents; all you'd have to do is to copy and paste the code into an Rmarkdown document after installing RStudio and then using the `knit` button option for generating a Word document. [https://rmarkdown.rstudio.com/](https://rmarkdown.rstudio.com/) ...
written 10 weeks ago by Friederike5.2k
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Comment: C: how to confirm that mapped read are accurate?
... Are there any regions in the human genome that are very similar to your virus of interest? If you use the viral genome you used as a a reference and cut it up into fake "short read" sequences and align it against the human, where do they go? And what are the alignment scores of the real reads that a ...
written 10 weeks ago by Friederike5.2k

Latest awards to Friederike

Scholar 5 weeks ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: More than 300.000 peaks for a viral transcription factor - what could this mean?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
Scholar 3 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: More than 300.000 peaks for a viral transcription factor - what could this mean?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Scholar 6 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Scholar 6 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Scholar 6 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Scholar 6 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: More than 300.000 peaks for a viral transcription factor - what could this mean?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ

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