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Comment: Overlap File for RACON Genome Polisher
Overlap File for RACON Genome Polisher
Answer: LD-prune variants while maintaining a list of SNPs
Comment: TaxID mapping file
Answer: LD-prune variants while maintaining a list of SNPs
Comment: Downloading full alignments from Pfam
Answer: Segmentation error while using a tool
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Recent Replies
Answer: install package
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Mathew
▴ 30
Hi, This is what happens when I run some code to diagnose the issue. First, I wanted to see what version of R was required for the package…
Comment: TaxID mapping file
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Lada
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thank you, I'll look at these files/documents. .
Answer: LD-prune variants while maintaining a list of SNPs
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Jautis
▴ 540
I was given a solution by a colleague -- it seems a little hacky, but worked really well! > one way to get this to work is to use --clu…
Answer: Association study using SNP data
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drajangirija
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Hi Matthew, Thank you very much for your inputs. I am working with Neogen genotyping data, which includes GC values less than 0.15.
Comment: Downloading full alignments from Pfam
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bef1
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I tried contacting Pfam, they replied that indeed there is an issue on their side with the full alignments, which should be repaired in the…
Comment: Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Expe
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Mensur Dlakic
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Don't know about others, but I would never contact someone about potential employment based only on their interests and with zero knowledge…
Comment: The GDC Legacy Archive is retiring soon.
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Zhenyu Zhang
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If you are talking about methylation idat files, they were all migrated from legacy to the data portal. If you are talking about other pl…
Comment: How to access TCGA samples that were treated with a specific drug?
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These TCGA samples were taken 10 ~ 20 years ago, and there is no way they have been treated by the modern immunotherapy. Are you sure tha…
Comment: Design matrix Differential expression analysis
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Gordon Smyth
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> When is it recommended to use the design <- cbind(Intercept=1,Group=c(-1,-1,-1,1,1,1)) It is not recommended. No such code appears anywh…
Comment: GRCh38.gmap file
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lorena9132
▴ 10
Hi Mathew, The .txt files provided in the link differ from the .gmap files, but after several attempts, I succeeded in generating the .gma…
Answer: GRCh38.gmap file
by
Mathew
▴ 30
Hi, I have spent some time searching for a GRCH38 map file for you. I have found a certain publication that uses a hg38 genetic map file…
Answer: Association study using SNP data
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Mathew
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Hi, You asked three questions so I will attempt to help the best I can **What should be the optimal GC score cutoff** It sounds li…
Comment: Design matrix Differential expression analysis
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SHN
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Thank you for your explanation. I am working on the cell lines and I am investigating the effect of the treatment on the expression level, …
Answer: Issues with Mixture file when using CIBERSORTx
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vjanve
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I ran into same issue of "duplicated gene symbol(s)": 1: In CIBERSORTxFractions(sigmatrix = sigmatrix, mixture = mixture, : 22292 dup…
Comment: creating batch colum for batch correction
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Expert
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Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
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