User: cpad0112
cpad0112 • 5.2k
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Posts by cpad0112
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C: Error for reading .gtf file in R
... It seems program has a trouble in reading gtf from gencode (both primary and main). I checked both v22 and v28 (latest). Alternate is to use gtf from Ensembl:. If you don't want to use ensembl annotations, i have provided another way to use the gencode gtf. For using Ensembl annotation, Download gtf ...
written 15 hours ago by
cpad0112 • 5.2k
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... Original VCF was functionally annotated with [VEP][1] as the tags in the OP (original post) are inline with VEP output. Duplicate entries you have posted at the start are not present in VCF file you have shared. Apparently, that duplicate p syntax might be due to multiple transcripts being affecte ...
written 18 hours ago by
cpad0112 • 5.2k
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... @fibar: post example file list. File list you have and code you are using. please don't post screenshots unless it is error. ...
written 19 hours ago by
cpad0112 • 5.2k
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Comment:
C: Error for reading .gtf file in R
... I think this issue is same as: https://www.biostars.org/p/313777/. Instead of Rstudio, try the code in R console. ...
written 22 hours ago by
cpad0112 • 5.2k
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... Well, this is not an answer to OP issue. But do update R. It is 3.1.2 and current version is 3.5. It could be as simple as antivius + google desktop indexing as described here https://stackoverflow.com/questions/5700505/windows-7-update-packages-problem-unable-to-move-temporary-installation and htt ...
written 1 day ago by
cpad0112 • 5.2k
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... I think OP is on OS X.
last line from error (copy/pasted):
Command "/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python -u -c "import setuptools, tokenize;__file__='/private/var/folders/tz/89qgqyd97wj1cdrpq_d62n100000gr/T/pip-install-qZhLf2/pysa ...
written 1 day ago by
cpad0112 • 5.2k
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... 1. Please navigate to samtools folder where samtools executable is present and type `./samtools.` If it works, then you have samtools binary
2. Once it works, then type `realpath samtools`
3. Then type `echo $PATH`
Output from realpath should be in path output. ...
written 1 day ago by
cpad0112 • 5.2k
0
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95
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... @OP: Locate the folder where the samtools is installed. Add that folder path to your .bash_profile or .bashrc. ...
written 1 day ago by
cpad0112 • 5.2k
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... Probably as separate x and y chromosomes ...
written 1 day ago by
cpad0112 • 5.2k
1
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120
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Answer:
C: listing library names
... Any one them:
$ parallel echo {= s/\\..*// =} ::: *.gz| sort -ur
$ for i in *.gz; do echo ${i%%.*};done | sort -ur
$ ls *.gz| cut -f1 -d"." | sort -ur ...
written 1 day ago by
cpad0112 • 5.2k
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For A: .fai file generation for a vcf file containing snps
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For A: convert SNP calls to amino acid change
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For A: which feature is considered as expression level ?
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For A: convert SNP calls to amino acid change
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For C: Problem installing Rgraphviz in R
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For C: can someone read this result to me
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For C: can someone read this result to me
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For A: .fai file generation for a vcf file containing snps
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For A: .fai file generation for a vcf file containing snps
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For A: .fai file generation for a vcf file containing snps
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Teacher
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For A: convert SNP calls to amino acid change
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For A: .fai file generation for a vcf file containing snps
Teacher
5 months ago,
created an answer with at least 3 up-votes.
For A: convert SNP calls to amino acid change
Teacher
5 months ago,
created an answer with at least 3 up-votes.
For A: convert SNP calls to amino acid change
Scholar
5 months ago,
created an answer that has been accepted.
For A: .fai file generation for a vcf file containing snps
Good Answer
5 months ago,
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For C: can someone read this result to me
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For C: can someone read this result to me
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For A: .fai file generation for a vcf file containing snps
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