User: rthapa
rthapa • 0
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Posts by rthapa
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... 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 ...
written 4 weeks ago by
rthapa • 0
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... 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
rthapa • 0
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... 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
rthapa • 0
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... SNPs.bed: ASCII text
genesgff1.bed: ASCII text
...
written 11 weeks ago by
rthapa • 0
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190
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... It looks like it printed out every line of the file. ...
written 11 weeks ago by
rthapa • 0
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... 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
rthapa • 0
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... 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
rthapa • 0
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... 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
rthapa • 0
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... 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 ...
written 11 weeks ago by
rthapa • 0
• updated
11 weeks ago by
Pierre Lindenbaum ♦ 127k
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... 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 ...
written 3 months ago by
rthapa • 0
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For transcript count after string tie merge
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