User: Ana

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Ana20
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Posts by Ana

<prev • 37 results • page 1 of 4 • next >
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conditional replacing rows with 9
... I have a directory containing nearly 11 million small SNPs files: like this wa_filtering_DP15_good_pops_snps_file_1 wa_filtering_DP15_good_pops_snps_file_2 . . . wa_filtering_DP15_good_pops_snps_file_11232111 and each file has only 2 rows (first row allele count for the wil ...
text-processing bash written 1 day ago by Ana20 • updated 1 day ago by st.ph.n1.6k
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Comment: C: 012 genotype matrix using vcf tools (converting rows to columns)
... So I created this little Rscript and got my desired output, thanks Kevin for sharing your experience with me: > #!/usr/bin/Rscript > > snps<-read.delim('wild_annuus.snps.fb.lenient.noTE_filt_DP15_GOOD_IND_ld.pruned.0.1._replaced_9.geno.table.012',header=F,row.na ...
written 11 days ago by Ana20
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Comment: C: 012 genotype matrix using vcf tools (converting rows to columns)
... Hi @Kevin Blighe, Thanks. The the example above is just with subset of the data. yes! you are right, did you also get output with "V" prefix? By the way I found the solution, It works ... thanks so much ...
written 11 days ago by Ana20
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Comment: C: SnpMatrix from VCF file
... Hi@Pierre Lindenbaum. I am also facing with the same problem as @Dhana. I have a filtered vcf file and I want to create something exactly similar to SNP.txt file that @Dhana showed above. Does this script has been created for this purpose? I could not get very well what is the input format of @Dhan ...
written 11 days ago by Ana20
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Comment: C: 012 genotype matrix using vcf tools (converting rows to columns)
... Hi @Kevin Blighe, thank you for your response. Well are you sure that you could transpose 012 genotype matrix created by vcf-tools in R? This is my out pot from vcf file (012-out) > 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 0 0 0 0 0 1 0 0 0 0 0 0 -1 0 -1 -1 -1 0 0 -1 -1 -1 and R cannot ...
written 11 days ago by Ana20
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how to print a specific column condition in multiple files
... I have a bunch of files (=2181;anacovis2_1_summary_betai_reg.out to anacovis2_2181_summary_betai_reg.out) which are the results of my genome scan test, below are a few of the anacovis2_2_summary_betai_reg.out anacovis2_3_summary_betai_reg.out anacovis2_4_summary_betai_reg.out anacov ...
unix text-processing written 12 days ago by Ana20 • updated 12 days ago by Kevin Blighe1.1k
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012 genotype matrix using vcf tools (converting rows to columns)
... Hello everyone, I have created a 012 genotype matrix by using --012 command in vcf tools which give individuals in row and SNPs in columns. I want to run smartpca and and need to convert rows to columns. Means get SNPs in rows and individuals in columsn. I have tried some shel commands like this but ...
vcf-tools genotype matrix written 16 days ago by Ana20 • updated 11 days ago by Kevin Blighe1.1k
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012 genotype matrix using vcf tools
... Hello everyone, I have a vcf-file contains nearly 11millions SNPs. I want to convert my vcf file into 012 genotype matrix for LD pruning. I am using this code: /data/programs/vcftools_0.1.13/bin/vcftools --vcf my.file.vcf --012 --out output_geno.vcf So, I get the output, but I am confu ...
vcf tools genotype matrix columns written 23 days ago by Ana20
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Comment: C: error with running distruct.py in fastSTRUCTURE
... Yes, I am quite sure. I've checked many times; 4.0K -rw-r----- 1 shsoudi shsoudi 930 Aug 13 14:07 random1_10K_genotype.5.log 476K -rw-r----- 1 shsoudi shsoudi 474K Aug 13 14:07 random1_10K_genotype.5.meanP 16K -rw-r----- 1 shsoudi shsoudi 16K Aug 13 14:07 random1_10K_genotype.5.m ...
written 4 weeks ago by Ana20
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error with running distruct.py in fastSTRUCTURE
... Hi everyone, I am trying to visualize the expected admixture proportions inferred by fastStructure by using python distruct.py This is the command that I am running: python /global/software/faststructure/faststructure_20150319/distruct.py -K 5 --input=${GENO} --output=${OUT} But I get this er ...
faststructure admixture proportions written 4 weeks ago by Ana20

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