User: Alex S

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Alex S0
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Posts by Alex S

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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 11 weeks ago by Alex S0
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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 11 weeks ago by Alex S0
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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 12 weeks ago by Alex S0
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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 12 weeks ago by Alex S0
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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 12 weeks ago by Alex S0
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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 3 months ago by Alex S0
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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 4 months ago by Alex S0
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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 4 months ago by Alex S0

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