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Tutorial:
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Recent Replies
Comment: Integrated Seurat object change name of the two conditions
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Amitm
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Hi,
See this [prev. post][1] where I contributed to, on accessing the meta data slot in a seurat object. There is more than one way.
[1…
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jared.andrews07
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I appreciate this statement and it largely mirrors my own. Lior sometimes makes extremely salient and important points. Other times, he's t…
Comment: Highly inflated p-values in GWAS by regenie
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cwwong13
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Thanks @4galaxy77 . The first 10 PCs were included in the calculation of the trait residuals, but still results were highly inflated.
Comment: Hisat2 index and alignment question
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Istvan Albert
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the most logical and simple explanation is that most likely the path to index is specified incorrectly
show us the paths with say `ls` the…
Comment: How to change from gene_id to GeneID/EntrezID using R
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Kevin Blighe
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It would have been good if you had mentioned the species in your opening question.
Regarding the fact that it may not be related to Ensembl…
Comment: How to change from gene_id to GeneID/EntrezID using R
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Nicolas
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Thank you for your help but my data are not related to ENSMBL and im not working with any model organism that allow me to use the org packa…
Comment: How to change from gene_id to GeneID/EntrezID using R
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Nicolas
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The thing is that every tutorial i've seen here is about using biomrt but as i said my data are not related to ENSMBL and i dont have the c…
Answer: Hugo_Symbol to Entrez ID
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It is likely that many of these genes have no corresponding Entrez Gene ID. Entrez (NCBI), HUGO, and Ensembl have different 'rules' about h…
Answer: How to change from gene_id to GeneID/EntrezID using R
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Kevin Blighe
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Hello,
A solution that may help: https://www.biostars.org/p/9461782/#9461790
By the way, if you are using *topGO* for the enrichment,…
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blz
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Is it not an option just to add the path to write sam and summary files on fastq files directory (or anywhere you want)?
hisat2 -p 8 -…
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fyi, I went ahead and took care of the vcf2phylip task for ploidy <= 2 last week, by adding a phylip exporter to plink2 that is functionall…
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chrchang523
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For one sample, a simple way to do this is to filter for minor-allele-count <= 0:
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- Note that 15 is always too low of a length limit. Even without the "chr" prefix, there are lots of SNPs on e.g. chr10 with POS > 9999999…
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Thank you for your contributions https://www.biostars.org/u/30020/ much appreciated.
I would also say that when it comes to science we sh…
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something like this ? create new two columns , sort on those columns, reverse the format.
awk -F '_' '/^>/ {cluster=$0;next;} {pri…
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