User: dago

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dago2.6k
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Posts by dago

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Comment: C: R: download all KEGG pathways including KO and Compounds
... I did not think about this. I guess I an getting used to have open source tools/db. Thanks ...
written 4 months ago by dago2.6k
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Comment: C: R: download all KEGG pathways including KO and Compounds
... ah right, that is maybe why I could not find any tool doing that! ...
written 4 months ago by dago2.6k
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Comment: C: R: download all KEGG pathways including KO and Compounds
... That is actually great! But I am not sure there are compounds here, just name of genes. No? ...
written 4 months ago by dago2.6k
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R: download all KEGG pathways including KO and Compounds
... I saw this question has been asked here and there before. However, I could not find a tool that does the job for me. I want to download all pathways from KEGG including KO and compounds using R. I would imagine creating an R object like: $Path_1 ...KO ...Compounds $Path_2 ...KO ...
R system_biology kegg written 4 months ago by dago2.6k • updated 4 months ago by ATpoint40k
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Comment: C: gatk v4.14.0 does not recognize matematical operators
... Thank you @Amar, I appreciate your suggestions. I tried what you said as well 20.0, 20, 20.00. Always the same. I personally believe that there is an issue with Java. ...
written 12 months ago by dago2.6k
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Comment: C: gatk v4.14.0 does not recognize matematical operators
... Sorry, I did that as well, but I still get the same error. I edit my post now ...
written 12 months ago by dago2.6k
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Comment: C: gatk v4.14.0 does not recognize matematical operators
... I also posted this issue on the gatk github, sorry for the double posting ...
written 12 months ago by dago2.6k
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Comment: C: gatk v4.14.0 does not recognize matematical operators
... Thanks for your comment. I jsut tried and it gives me the same error. ...
written 12 months ago by dago2.6k
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gatk v4.14.0 does not recognize matematical operators
... Dear all I have problem with filtering the SNPs called with gatk v4.1.4.0. I have a vcf file that looks like this: contig00001 8227 . A G 40.68 . AC=1;AF=0.100;AN=10;BaseQRankSum=-0.861;ClippingRankSum=0.000;DP=88;FS=13.035;MLEAC=1;MLEAF=0.100;MQ=60.00;M ...
java snp written 12 months ago by dago2.6k
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Answer: A: How to tell whether an MSA result is good and how to set parameters?
... I think there are different approaches to asses the alignments: [A statistical score for assessing the quality of multiple sequence alignments][1] [Automatic assessment of alignment quality][2] However, I personally never really dug too much into it. For two main reasons: 1. I am often familiar ...
written 13 months ago by dago2.6k

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