User: mbk0asis

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mbk0asis360
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Posts by mbk0asis

<prev • 116 results • page 1 of 12 • next >
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Comment: C: Can I obtain data of individula's called variants from 1000 genome project?
... Opps! How did I miss that? Thank you, Kevin! ...
written 2 days ago by mbk0asis360
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(Closed) Can I obtain data of individula's called variants from 1000 genome project?
... Hi. As mentioned in the title, I'd like to obtain the Exome-seq data from the 1000 genome project in VCF. But I couldn't find them. VCF files I found seemed to have the combined variant data. Am I missing something here? Or they just don't have the variant called data of individuals? Thank y ...
vcf 1000 genome exome-seq written 2 days ago by mbk0asis360
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Meaning of mfold upper limit?
... Hi, all! I've been working on ChIP-seq data using 'MACS2', and am confused by "mfold". Does "mfold" represent the relative enrichment against control (IgG or genomic fragments) or background noises in the test sample? And why there's a upper limit in "mfold"? Does that mean fold-enrichment over a ...
mfold macs2 chip-seq written 10 days ago by mbk0asis360
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Answer: C: How can I download the fasta file of RepeatMasker UCSC table directly?
... I don't think you can download repetitive sequences directly from UCSC genome browser as genomax mentioned. Instead, get the bed file of RepeatMasker and whole genome sequence of your organism from UCSC genome browser, and use 'bedtools getfasta' to extract the sequences of retroelements. ...
written 20 days ago by mbk0asis360
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Comment: C: Is there any method to run tophat ?
... [Check out this][1] thread to run mutiple files using an alignment tool, and switch to 'Hisat2' or something else as people are saying! [1]: https://www.biostars.org/p/223404/ ...
written 20 days ago by mbk0asis360
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how to interpret imputed/phased VCF?
... Hi. I have several vcf files contain imputed/phased variant calls download from [HipSci.][1] They say they used IMPUTE2 for imputation, so the files have the information like below. X 65179 . G C IMP2=0.474,0.864,0.93 GT:GP:PS 0|1:0.061,0.93,0.009:60034 X ...
vcf imputed phased written 25 days ago by mbk0asis360
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Comment: C: P-value calculation for Gene Ontology Terms
... [Check here][1] [1]: https://www.researchgate.net/post/How_to_calculate_the_p-Value_in_gene_ontology_analysis ...
written 5 weeks ago by mbk0asis360
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deepTools - change line colors in profile plots above a heatmap
... Hi. I've generated a heatmap with profile plots above it using 'deepTools'. The heatmap is clustered into 2 groups using '--kmeans' option. The heatmap looks OK, but lines in the profile plots, especially, cluster2 lines are too faint to see. Is there a option to change the colours? Thank you! ! ...
deeptools profile plot heatmap written 5 weeks ago by mbk0asis360 • updated 5 weeks ago by Devon Ryan82k
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Comment: C: How to get plasmid or costruct sequence from fastq file in c.elegans Whole-genom
... Map the fastq on construct. Extract mapped reads. Trim off the plasmid sequences. Map the remaining part of genomic sequence to reference genome. That's my rough idea. ...
written 8 weeks ago by mbk0asis360
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Can I combine sessions saved in UCSC genome browser?
... Hi. UCSC genome browser let us save genomic data as 'sessions' and access the data anytime anywhere. I really like the feature, but sometimes I need to compare data saved in different sessions. I wonder if there is a way to combine UCSC genome browser sessions to load multiple sessions in one page ...
sessions ucsc genome browser written 8 weeks ago by mbk0asis360

Latest awards to mbk0asis

Popular Question 20 days ago, created a question with more than 1,000 views. For overlapping texts (plot.PCA in FactoMineR)
Popular Question 5 weeks ago, created a question with more than 1,000 views. For overlapping texts (plot.PCA in FactoMineR)
Popular Question 9 weeks ago, created a question with more than 1,000 views. For overlapping texts (plot.PCA in FactoMineR)
Centurion 11 weeks ago, created 100 posts.
Popular Question 4 months ago, created a question with more than 1,000 views. For overlapping texts (plot.PCA in FactoMineR)
Popular Question 7 months ago, created a question with more than 1,000 views. For overlapping texts (plot.PCA in FactoMineR)
Scholar 7 months ago, created an answer that has been accepted. For A: select DE genes
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Subsetting DESeq2 results by padj quantity
Student 11 months ago, asked a question with at least 3 up-votes. For Pairwise2 - Biopython - weird local alignment results
Popular Question 11 months ago, created a question with more than 1,000 views. For fasta - reverse complement sequence
Popular Question 13 months ago, created a question with more than 1,000 views. For fasta - reverse complement sequence
Scholar 13 months ago, created an answer that has been accepted. For A: select DE genes
Popular Question 17 months ago, created a question with more than 1,000 views. For Finding a sequence in a fasta file
Great Question 18 months ago, created a question with more than 5,000 views. For Finding a sequence in a fasta file
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Popular Question 2.0 years ago, created a question with more than 1,000 views. For Pairwise2 - Biopython - weird local alignment results
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Popular Question 3.0 years ago, created a question with more than 1,000 views. For Finding a sequence in a fasta file

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