User: igor

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igor5.6k
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Posts by igor

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Answer: A: Cell type assignment in single-cell RNAseq
... This is actually more difficult than it may sound at first. There are a few suggestions in this previous thread: https://www.biostars.org/p/294375/ ...
written 1 day ago by igor5.6k
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Answer: A: Processing GTEx RNA-Seq data using the TCGA bioinformatic pipeline
... You should consider using RNAseqDB where they analyzed TCGA and GTEx data together (and even applied batch correction): https://github.com/mskcc/RNAseqDB ...
written 1 day ago by igor5.6k
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Answer: A: Builiding reference for annovar based on build37.1?
... It would probably be a lot easier to convert your VCF to hg19 than to prepare the ANNOVAR input for your reference, especially if you want to use more than just gene info (ANNOVAR has a lot of other pre-built databases). See this earlier discussion: https://www.biostars.org/p/309708/ ...
written 3 days ago by igor5.6k
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Comment: C: Builiding reference for annovar based on build37.1?
... I am not sure ANNOVAR can download from arbitrary URLs. It needs files to be in a specific format. ...
written 3 days ago by igor5.6k
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Comment: C: build37 against hg19
... You can try CrossMap to convert the VCF to the desired build: http://crossmap.sourceforge.net/ ...
written 3 days ago by igor5.6k
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Answer: A: build37 against hg19
... You should spot-check the variants that get successfully annotated (in a genome browser). Do those make sense? That will tell you if the annotation is working properly. It's possible that all the "dots" you see are non-coding. Depending on how the variants were called, it's possible that most of th ...
written 3 days ago by igor5.6k
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Comment: C: differential expression analysis from microarray data
... Have you tried running `topTable()` without `lfc` parameter? This way you can see the distribution of your fold changes. Maybe none of the negative fold changes are more than 2. ...
written 3 days ago by igor5.6k
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Comment: C: convert amino acids between species
... Thanks! I actually was not aware. But is there a better way than parsing pages like this? https://www.ncbi.nlm.nih.gov/homologene?cmd=Retrieve&dopt=MultipleAlignment&list_uids=460 ...
written 4 days ago by igor5.6k
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Answer: A: CNV detection from RNA-seq data
... I just found [HoneyBADGER][1], another method for single-cell RNA-seq: > HoneyBADGER (hidden Markov model integrated Bayesian approach for > detecting CNV and LOH events from single-cell RNA-seq data) identifies > and infers the presence of CNV and LOH events in single cells and > recon ...
written 4 days ago by igor5.6k
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convert amino acids between species
... The mouse homolog of TP53 is Tp53, but the specific sequence is obviously slightly different and the mouse equivalent of human R249S is R246S. For a few mutations, it's relatively simple to align the two gene sequences and visually inspect how they line up, but this is not really feasible if you hav ...
gene amino acid homology variants written 4 days ago by igor5.6k

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Teacher 16 days ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Commentator 16 days ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Epic Question 5 weeks ago, created a question with more than 10,000 views. For ATAC-seq peak calling with MACS
Scholar 6 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
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Popular Question 9 weeks ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
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Popular Question 4 months ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Popular Question 4 months ago, created a question with more than 1,000 views. For Best way to perform single-cell RNA-seq normalization
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