User: dec986

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dec986260
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Posts by dec986

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Comment: C: Correct command line syntax for plink2
... I'm having a really hard time getting all of the plink input files ready. /Scripts/plink1.9/plink --vcf genetic-data/ZZFNMDMF.vcf.gz --out ZZFNMDMF --make-founders --make-bed generates .nosex, .log, .bed, .fam, .bin files. However, I cannot generate the ped file that is also required: 703404 ...
written 10 weeks ago by dec986260
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Correct command line syntax for plink2
... Hello, I'm running PLINK v2.00a2.3LM 64-bit Intel (24 Jan 2020) and I cannot get the command line syntax correct for LD pruning. I've been reading https://avikarn.com/2019-07-30-prunning/ and https://www.cog-genomics.org/plink/2.0/ld but am confused about what I've read there. There are no exampl ...
plink2 written 10 weeks ago by dec986260 • updated 10 weeks ago by chrchang5237.7k
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Answer: A: Differentially methylated regions: Easy & Fast Identification and ANnoTation
... hi @vechtova are you able to send the files on Google Drive? My email is dec986@gmail.com I have a little more than 6 GB available, that should be more than enough for 6 files if you tarball them ("tar cvjf"). Does that method work for you? ...
written 11 weeks ago by dec986260
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Comment: C: Differentially methylated regions: Easy & Fast Identification and ANnoTation
... Hi @vechtova, Unfortunately, I'm unable to reproduce your exact error with my sample data. Could you try a script with the following commands: $DEFIANT -i $T0R1,$T0R2,$T0R3 $T24R1,$T24R2,$T24R3 $DEFIANT -L T0,T24 -i $T0R1,$T0R2,$T0R3 $T24R1,$T24R2,$T24R3 $DEFIANT -b -i $T0R1,$T0R2,$T0 ...
written 12 weeks ago by dec986260
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Comment: C: Differentially methylated regions: Easy & Fast Identification and ANnoTation
... Hi @vechtova this error occurs if there is a point with 0 coverage (which will lead to undefined methylation values). In other words, these CpG were not detected. Would you be able to eliminate these from your data? Let me know if this fixes your problem. ...
written 12 weeks ago by dec986260
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Comment: C: Differentially methylated regions: Easy & Fast Identification and ANnoTation
... Hi @vechtova, that's interesting, I haven't encountered this before. The problem is that the "chr" string helps Defiant to identify which input type is present. I think that I can try to change this, but it will take a few days. As a short workaround, something like the script below can add "chr" ...
written 12 weeks ago by dec986260
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Answer: A: vcftools not outputting any file, and not giving any error message
... the problem was that vcftools needs `recode` to have output at all. vcftools --exclude-positions X.bed --gzvcf merged.vcf.gz --out merged.noX --recode ...
written 4 months ago by dec986260
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vcftools not outputting any file, and not giving any error message
... Hello, I'm running this vcftools command on a 148 GB vcf.gz flie: > nohup vcftools --exclude-positions X.bed --gzvcf merged.vcf.gz --out merged.noX & the bed file was made with vcf2bed. however, even after about 15 minutes, there is no output except a log file, and the program keeps runni ...
vcftools written 4 months ago by dec986260
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How to Interpret Chromosome Names from
... I have downloaded data thus: wget 'ftp://ftp.ncbi.nih.gov/snp/latest_release/VCF/GCF_000001405.25.gz' which gives strange chromosome names: NC_000001.10 and NC_000002.10, NC_000003.10 Can I interpret these chromosomes as 1, 2, and 3 respectively? ...
genome written 4 months ago by dec986260 • updated 4 months ago by JC12k
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how to add reference alleles to VCF?
... I’m converting gVCFs to VCF, but the reference alleles are missing. An example below: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 180525_FD02929177 1 97547947 . T . . . DP=31 GT:DP:RGQ 0/0:31:81 1 97915614 . C . . . DP=40 GT:DP:RGQ 0/0:40:99 1 97981343 . A . . . DP=43 GT:DP:RGQ 0 ...
vcf genome written 5 months ago by dec986260 • updated 5 months ago by Ram32k

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