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: How I know a file is sam or bam, sorted or unsorted
... So it was a problem with the memory. It'd be great if you could accept the answer that suggested that so that other users in the future will be pointed to the right track immediately. ...
written 5 months ago by Friederike5.2k
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Comment: C: convert VCF to gVCF
... >My goal is to extract all SNPs, not just the variations from reference. What do you mean by that? How were the SNPs determined in the first place if not by comparing your sequencing results to the reference genome? ...
written 5 months ago by Friederike5.2k
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Comment: C: R error: vector memory exhausted
... Don't you want `#NA / all` <= 0.05 then? ...
written 5 months 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 5 months 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 5 months ago by Friederike5.2k
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Comment: C: List of plant long read genome assemblies
... Where have you looked so far? ...
written 5 months 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 5 months 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 5 months 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 5 months 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 5 months ago by Friederike5.2k

Latest awards to Friederike

Scholar 4 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
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 5 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 5 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 6 months ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
Scholar 7 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
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
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?
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Understanding ATAC-seq data
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
Teacher 9 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 9 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 9 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Scholar 9 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Teacher 9 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 9 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Teacher 9 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 9 months ago, created an answer that has been accepted. For A: epigenetic database for immuncells
Teacher 10 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 10 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?

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