Moderator: ATpoint

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ATpoint28k
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Posts by ATpoint

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Answer: C: RSEM installation Errors
... You can always install via conda if compilation fails: https://anaconda.org/bioconda/rsem This does not solve the compilation problem itself but saves you time to focus on what is important: Your analysis. ...
written 1 hour ago by ATpoint28k
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Comment: C: mouse oncogene database
... Hello Sara! Questions similar to yours can already be found at: database for mouse tumor supressor genes and oncogenes We have closed your question to allow us to keep similar content in the same thread. If you disagree with this please tell us why in a reply below. We'll be ha ...
written 2 hours ago by ATpoint28k
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Comment: C: RNA seq analysis; two samples
... Please use the search function and google for advice on experiments without replicates. There are literally dozens of threads on this. Also check the manuals of the established tools, most have a section that covers it. ...
written 2 hours ago by ATpoint28k
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Comment: C: (scRNA) bustools transcript to gene file
... There is a kallisto user group https://groups.google.com/forum/#!forum/kallisto-and-applications where you could ask for expert clarification, just fyi. ...
written 3 hours ago by ATpoint28k
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Comment: C: (scRNA) bustools transcript to gene file
... Are they aligned to cDNA? I always quantify against the entire transcriptome (with salmon/alevin though). THere is no strict rule that only coding transcripts must be used. Differential regulation of ncRNAs might/is/can-be biologically meaningful as well. I would exclude small RNAs though before DEG ...
written 5 hours ago by ATpoint28k
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Answer: C: How to decrease the number of candidate TFs binding to gene promoter region
... I would get my hands on RNA-seq data from the cell type you are working on and then eliminate factors lowly-expressed in this cell type. Proteomics data would of course be more precise. You can also try to perform some kind of correlation analysis if you get your hands on larger (many samples) datas ...
written 6 hours ago by ATpoint28k
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Comment: C: Tool to design Q-PCR primers with exon skipping?
... Can't you construct a dummy cDNA and feed this into PrimerBLAST? If exonB is skipped then make a sequence that does not contain it. This still would have all the benefits from PrimerBLAST which you need for a reliable qPCR primer. ...
written 7 hours ago by ATpoint28k
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Comment: C: How to find both primers on reads?
... Please a representative input an output example. People are typically relucant to go through multiple lines of your just tounderstand the problem. A good illustration always helps. ...
written 7 hours ago by ATpoint28k
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Comment: C: How to analyze the RNAseq paired samples with DESeq2?
... If you aim to promote your tool, please make a `Tool` post. OPs question is not about this. I will therefore move it to comment. Please do not advertise your tool if it doesn't add to the question. ...
written 7 hours ago by ATpoint28k
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Comment: C: ATAC-seq sample normalization (quantil normalization)
... Our of interest, is there a reference for normalizing per-million scaled data with QN rather than raw counts? From what I understand, e.g. [here][1], one starts typically from integers, no? Or doesn't it make a difference? Not a statistician myself at all as you can see, so correct me if wrong. htt ...
written 7 hours ago by ATpoint28k

Latest awards to ATpoint

Appreciated 7 hours ago, created a post with more than 5 votes. For C: Detect repeats problematic for PCR
Scholar 22 hours ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Teacher 5 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Teacher 5 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Teacher 5 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Scholar 7 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Teacher 8 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Scholar 8 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Good Answer 9 days ago, created an answer that was upvoted at least 5 times. For C: Detect repeats problematic for PCR
Teacher 10 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Appreciated 12 days ago, created a post with more than 5 votes. For C: Detect repeats problematic for PCR
Scholar 13 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Teacher 14 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Scholar 14 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Epic Question 14 days ago, created a question with more than 10,000 views. For Fast download of FASTQ files from the European Nucleotide Archive (ENA)
Scholar 17 days ago, created an answer that has been accepted. For C: Mapping reads to nuclear, chloroplast, and mitochondria genome separately but al
Teacher 17 days ago, created an answer with at least 3 up-votes. For C: Mapping reads to nuclear, chloroplast, and mitochondria genome separately but al
Scholar 17 days ago, created an answer that has been accepted. For C: Mapping reads to nuclear, chloroplast, and mitochondria genome separately but al
Teacher 18 days ago, created an answer with at least 3 up-votes. For C: Mapping reads to nuclear, chloroplast, and mitochondria genome separately but al
Scholar 19 days ago, created an answer that has been accepted. For C: Mapping reads to nuclear, chloroplast, and mitochondria genome separately but al
Teacher 20 days ago, created an answer with at least 3 up-votes. For C: Mapping reads to nuclear, chloroplast, and mitochondria genome separately but al
Scholar 20 days ago, created an answer that has been accepted. For C: Mapping reads to nuclear, chloroplast, and mitochondria genome separately but al
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: Mapping reads to nuclear, chloroplast, and mitochondria genome separately but al
Scholar 4 weeks ago, created an answer that has been accepted. For C: Mapping reads to nuclear, chloroplast, and mitochondria genome separately but al

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