User: moushengxu

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moushengxu260
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Posts by moushengxu

<prev • 157 results • page 1 of 16 • next >
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Comment: C: edgeR RNA-seq Results Across Conditions
... Can you post your code here? ...
written 5 weeks ago by moushengxu260
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Answer: A: Enrichment Analysis from DESeq2 data
... I use GSEA (Broad Institute). Just rank your genes by -log(P-value) * sign(logFC). ...
written 8 weeks ago by moushengxu260
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Comment: C: SNPEFF for de novo transcriptome annotation
... Well said! :) After returning the borrowed reference, make your own annotated genome the reference genome. ...
written 8 weeks ago by moushengxu260
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Answer: A: SNPEFF for de novo transcriptome annotation
... You need a reference genome. If you don't have a reference genome, maybe you can borrow one from a closest relative species. ...
written 8 weeks ago by moushengxu260
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Comment: C: snpEff inappropriate interpretation of variants?
... SnpEff version SnpEff 4.3p (build 2017-06-06 09:55), by Pablo Cingolani Looks the most recent? ...
written 8 weeks ago by moushengxu260
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Comment: C: snpEff inappropriate interpretation of variants?
... Awesome that you've found a transcript that codes for TNFRSF12A! As for the first example, does it actually mean the "interaction" is highly important, but whether the mutation makes any difference to the "interaction" is another matter? ...
written 8 weeks ago by moushengxu260
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Comment: C: functional variant discovery after GATK variant calling
... I am trying SnpEff and found some big problems: https://www.biostars.org/p/265016/. What's your experience in that aspect? Thanks! ...
written 8 weeks ago by moushengxu260
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Answer: A: adjusting p-value for GO analysis
... use FDR correction. In R, use: p.adjust(pval, method="fdr", ...) ...
written 8 weeks ago by moushengxu260
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Comment: C: snpEff inappropriate interpretation of variants?
... Really nicely formatted. Amazing. How did you achieve that? ...
written 8 weeks ago by moushengxu260
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snpEff inappropriate interpretation of variants?
... I have RNA-seq datasets, and I applied GATK variant calling procedure for RNA-seq (https://software.broadinstitute.org/gatk/documentation/article.php?id=3891). I have not found anything wrong with it yet. However, when I took the .vcf file output from GATK and used snpEff with GRCh 37.75 to assess t ...
software error variant calling alignment rna-seq written 8 weeks ago by moushengxu260 • updated 8 weeks ago by rbagnall1.1k

Latest awards to moushengxu

Popular Question 15 days ago, created a question with more than 1,000 views. For edgeR and GO analysis using goana
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: SNPEFF for de novo transcriptome annotation
Popular Question 4 months ago, created a question with more than 1,000 views. For edgeR and GO analysis using goana
Supporter 5 months ago, voted at least 25 times.
Centurion 6 months ago, created 100 posts.
Scholar 7 months ago, created an answer that has been accepted. For A: edgeR artifacts on p-value and/or fold change?
Scholar 11 months ago, created an answer that has been accepted. For A: edgeR artifacts on p-value and/or fold change?
Rising Star 11 months ago, created 50 posts within first three months of joining.

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