User: CandiceChuDVM

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CandiceChuDVM2.1k
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Posts by CandiceChuDVM

<prev • 57 results • page 1 of 6 • next >
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Comment: C: cellranger mkref failed
... I have added 10x genomics' solution below: ...
written 8 weeks ago by CandiceChuDVM2.1k
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Comment: C: cellranger mkref failed
... I encountered a similar problem. Here is 10x genomics' response: "It looks like the job failed in the STAR indexing step. This kind of failure is often caused by running out of memory. It could be a transient error or a limitation on the machine. You can try running it on a node with more availa ...
written 8 weeks ago by CandiceChuDVM2.1k
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Comment: C: How to perform edgeR based on serial paired samples?
... Hi Devon, When I apply `design <- model.matrix(~0 + subject + group)`, the `colnames(design)` are: [1] "subject1" "subject2" "subject3" "subject4" [5] "groupaffected_t2" "groupaffected_t3" "groupcontrol_t1" "groupcontrol_t2" [9] "groupcontrol_t3" ...
written 3.0 years ago by CandiceChuDVM2.1k
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How to perform edgeR based on serial paired samples? (model.matrix design)
... Hi all, I have 4 paired samples in treatment vs control at 3 different time points. How can I set up a `model.matrix` so I can treat them as paired samples and compare the following comparisons in `glmLRT` of edgeR: 1. Treatment vs control (paired samples), regardless of time 2. Treatment vs ...
R edger rna-seq written 3.0 years ago by CandiceChuDVM2.1k
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Answer: A: Small RNA-seq experimental design, pooling samples or not ? which one is better?
... Thanks for all replies. I think we have reached a conclusion that pooling isolated RNA is preferred over pooling biofluids. For the question "to pool or not to pool", the aforementioned papers only provide limited information. I've found another paper "[Experimental validation of methods for diff ...
written 3.1 years ago by CandiceChuDVM2.1k
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Comment: C: Small RNA-seq experimental design, which one is better?
... I understand your point. No doubt we should have as many biological replications as we can (I can have up to 10 per disease). Since you mentioned "without pooling", I was wondering how sample pooling would affect the statistical power if the numbers of lib. prep. are the same? Any reference? ...
written 3.1 years ago by CandiceChuDVM2.1k
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Small RNA-seq experimental design, pooling samples or not ? which one is better?
... Hi all, I have 3 types of diseases and one control group. Each disease has 10 samples. Ideally we would like to have individual library preparations (lib. prep.) for each sample, however, our budget won't be able to afford it. So that leaves us with one option: pooling samples. For sample pooling ...
pooling small rna-seq mirna-seq microrna rna-seq written 3.1 years ago by CandiceChuDVM2.1k • updated 24 months ago by BIOTECH.DEEPTI91110
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Comment: C: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
... Thanks! I wasn't aware of that. I will contact SRA later to figure out what to do at this point. ...
written 3.2 years ago by CandiceChuDVM2.1k
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Comment: C: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
... Yes. I have tried ftp using the following instruction: > After you login, > 1. navigate to your account folder: cd uploads/candicechu@tamu.edu_TsOpWGZR > 2. create a subfolder with a meaningful name (required): mkdir new_folder > 3. navigate to that folder: cd new_folder > 4. ...
written 3.2 years ago by CandiceChuDVM2.1k
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Comment: C: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
... I can't agree more with you. ...
written 3.2 years ago by CandiceChuDVM2.1k

Latest awards to CandiceChuDVM

Popular Question 2.4 years ago, created a question with more than 1,000 views. For Cuffdiff output ID list for gene ontology analysis in Panther
Popular Question 2.4 years ago, created a question with more than 1,000 views. For CummeRbund: unable to use getGenes to retrieve short names in R
Popular Question 2.4 years ago, created a question with more than 1,000 views. For How to interpret RseQC result for -r/--mate-inner-dist in Tophat2?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Is dog (Canis familiaris) transcriptome considered well-annotated?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Low DE genes in DESeq2 (update PCA plots)
Popular Question 2.4 years ago, created a question with more than 1,000 views. For miRDeep2: mapping produced bowtie.log and mapper.log - which one to trust?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For DESeq2 time course experiments: how to make plots for specific genes?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Can't group samples in StringTie for differential expression
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Small RNA-seq experimental design, pooling samples or not ? which one is better?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Inconsistency in Panther vs KOBAS2.0. Other recommendation for KEGG?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Low DE genes in DESeq2 (update PCA plots)
Appreciated 2.9 years ago, created a post with more than 5 votes. For Up-to-date RNA-Seq Analysis Training/Courses/Papers (Oct 2016)
Student 3.0 years ago, asked a question with at least 3 up-votes. For How to perform edgeR based on serial paired samples? (model.matrix design)
Epic Question 3.0 years ago, created a question with more than 10,000 views. For Up-to-date RNA-Seq Analysis Training/Courses/Papers (Oct 2016)
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Up-to-date RNA-Seq Analysis Training/Courses/Papers (Oct 2016)
Guru 3.2 years ago, received more than 100 upvotes.
Great Question 3.6 years ago, created a question with more than 5,000 views. For Up-to-date RNA-Seq Analysis Training/Courses/Papers (Oct 2016)
Gold Standard 4.1 years ago, created a post with more than 25 bookmarks. For Up-to-date RNA-Seq Analysis Training/Courses/Papers (April 2016)
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Up-to-date RNA Sequence Analysis Training/Courses/Papers?
Librarian 4.3 years ago, created a post with more than 10 bookmarks. For Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Prophet 4.3 years ago, created a post with more than 20 followers. For Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Appreciated 4.4 years ago, created a post with more than 5 votes. For Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?

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