User: Alex

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Alex0
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Posts by Alex

<prev • 9 results • page 1 of 1 • next >
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Answer: A: Help with Mitelman Database
... I ran into a similar problem. I had to inner join on KaryAbnorm and Cytogen to finally select the pubmed ids together with codes and abberations. The results correspond to the different references that are shown on Mitelman when clicking on an abberation. SELECT rec.ABERRATION as aberr ...
written 9 days ago by Alex0
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Comment: C: Converting SNP names from Illumina GSA array to rsID using PLINK
... I would also be interested in this. Have you had any success? ...
written 8 months ago by Alex0
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format
... Hi again Kevin, I have yet another question: On the final merge step (using data from the [1000g GRCH38 liftover release][1]) I encountered an error due to multiallelic sites > Error: 7650 variants with 3+ alleles present I tried - filtering to biallelic SNPs only in bcftools before anything ...
written 8 months ago by Alex0
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format
... Ha, the paper is an amazing reference for this topic, thanks for your help! By the way, I am using Snakemake to adapt/implement your tutorial above - I don't think you are, but if you're doing these workflows without using any workflow tool, check it out: http://snakemake.readthedocs.io/en/stable/t ...
written 8 months ago by Alex0
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format
... Thanks for your quick reply! I would have one more question if you would humor me - since I am still kind of coping with the basics, i'm afraid it's a little basic. Why do you constrain the data only to the coding strand? In Illumina GSA this would be entries with "+" in the 'RefStrand' column in ...
written 8 months ago by Alex0
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format
... Thanks for the great tutorial, it was very helpful! Since I have microarray data (Illumina) that I need to analyze: could you give any more information how you would approach the step **Exclude variants not on the coding strand**? ...
written 8 months ago by Alex0
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Answer: A: VCF files: Change Chromosome Notation
... Next to the above answers, this resource might be helpful: mappings between common notations (UCSC, Ensembl, Gencode) https://github.com/dpryan79/ChromosomeMappings You can use this together with awk 'NR==FNR{map[$1]=$2;next} { for (i=1;i<=NF;i++) $i=($i in map ? map[$i] : $i) } 1' mapping ...
written 9 months ago by Alex0
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Comment: C: Displaying somatic mutational signatures
... In particular, https://www.bioconductor.org/packages/release/bioc/vignettes/SomaticSignatures/inst/doc/SomaticSignatures-vignette.html#nik-zainal_mutational_2012 should be helpful with regards to normalizing between e.g. exome and whole genome. ...
written 10 months ago by Alex0
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Comment: C: Displaying somatic mutational signatures
... I am currently also confused by this statement. The way I currently interpret this is the following: Each published signatures seems to sum up to 1 over the 96 dimensions. This, I assume, refers to the "relative proportion of the mutations generated by each signature". This leaves the normalizatio ...
written 10 months ago by Alex0

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