User: rthapa

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rthapa0
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Posts by rthapa

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GWAS of ordinal phenotypes with MCMCglmm model
... Hi, I want to do genome-wide association studies of ordinal phenotypes (1,2,3,4,5). Since my phenotypic data is not continuous, I cannot use a generalized linear model. The few R packages I found are MASS:polr, ordinal package with clm function and MCMCglmm. It looks like polr and ordinal package c ...
R snp written 4 weeks ago by rthapa0
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Comment: C: error reading bed files for bedtools intersect
... It looks like the problem is from SNPs.bed file. In this file I can only have two columns - 1) Chromosome number and 2) SNP position but looks like bed file needs atleast 3 columns. I want to find the corresponding genes from gene annotation file by comparing gene location and SNP position. Do you h ...
written 11 weeks ago by rthapa0
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Comment: C: error reading bed files for bedtools intersect
... awk -F '\t' '(int($2)==0 || int($3)==0) {print FILENAME,NF,NR, $0;}' SNPs.bed It didn't display anything, which I think is correct. But still, bedtools intersect is not working. ...
written 11 weeks ago by rthapa0
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Comment: C: error reading bed files for bedtools intersect
... SNPs.bed: ASCII text genesgff1.bed: ASCII text ...
written 11 weeks ago by rthapa0
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Comment: C: error reading bed files for bedtools intersect
... It looks like it printed out every line of the file. ...
written 11 weeks ago by rthapa0
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Comment: C: error reading bed files for bedtools intersect
... It printed out number of lines. Is the error is due to this? How can I deal with this? SNPs.bed 2 1 Chr09 57068854 SNPs.bed 2 2 Chr09 57068854 SNPs.bed 2 3 Chr09 57068854 SNPs.bed 2 4 Chr06 13897772 SNPs.bed 2 5 Chr09 57068854 SNPs.bed 2 6 Chr02 2244737 SNPs.bed 2 7 Chr0 ...
written 11 weeks ago by rthapa0
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Comment: C: error reading bed files for bedtools intersect
... There were many lines with more than 4 fields. So, to simplify the file, I removed the last two columns and retained only the first two columns. cat -t SNPs.bed Chr09^I57068854 Chr09^I57068854 Chr09^I57068854 Chr06^I13897772 Chr09^I57068854 Chr02^I2244737 Chr09^I57068854 ...
written 11 weeks ago by rthapa0
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Comment: C: error reading bed files for bedtools intersect
... Thank you, I did remove the headers from both bed files. The output of cat genesgff1.bed SNPs.bed| awk -F '\t' '{print NF;}' | uniq | sort | uniq is 4 5 ...
written 11 weeks ago by rthapa0
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error reading bed files for bedtools intersect
... Hi, I am trying to use bedtools intersect to find the overlapping gene regions with corresponding SNPs. I have two files; SNP file and gene annotation file. I am getting the following error while using bedtools intersect. I do not see extra tab at the end of the lines, I am not able to find the prob ...
bedtools intersect written 11 weeks ago by rthapa0 • updated 11 weeks ago by Pierre Lindenbaum127k
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GO term using GOAtools
... Hi, I am getting a key error while reading the .obo file. The same script and obo file were working before. Does anyone have any suggestions? Thanks obofile = obo_par.GODag('go-basic.obo') Traceback (most recent call last): File "", line 1, in File "/Library/Frameworks/Python.fram ...
goatools written 3 months ago by rthapa0

Latest awards to rthapa

Popular Question 4 months ago, created a question with more than 1,000 views. For best value of lfc threshold
Popular Question 11 months ago, created a question with more than 1,000 views. For transcript count after string tie merge

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