User: paraskevopou

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paraskevopou20
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1 year, 7 months ago
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p***********@uni-potsdam.de

Posts by paraskevopou

<prev • 29 results • page 1 of 3 • next >
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Comment: C: estimate dN/dS ratio for multiple genes
... sorry spamming you again. Do you have any suggestions of which of the available models in KaKs-calculator package should I use? I though at the beginning that YN model should be sufficient but then I popped on a paper saying about all these γ model such as γ-YN and got a bit confused. MA model is t ...
written 13 months ago by paraskevopou20
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Comment: C: estimate dN/dS ratio for multiple genes
... My idea initially was to estimate the number of (SYN) and (NSY) per gene and then calculate the number of synonymous and non-synonymous sites in order to estimate dNdS. But, I realized that this is not that much straight forward. Now I used BCFtools consnsus to create the alternative reference. I cr ...
written 13 months ago by paraskevopou20
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(Closed) extract headers of a file using a second file containing a list of IDs
... Dear people! Sorry my question might be very trivial but I am very new in the bioinformatic field. I have a txt file containing the headers of a fasta file (file 1, 14000 headers) and a txt file, file2, with the IDs I want to extract. My problem is that this second txt file has only the TRINITY_ID ( ...
rna-seq written 13 months ago by paraskevopou20
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Comment: C: estimate dN/dS ratio for multiple genes
... sorry maybe the information was not precise. The real output is like this with the total length of the cds, the position of the SNP in the cds and the condon position of the SNP. I would like to avoid making alignments between reference and alternative and run PAML. Is there another way to estima ...
written 14 months ago by paraskevopou20
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estimate dN/dS ratio for multiple genes
... Hi all!! I would like to estimate dN/dS ratio per each of my genes seperately. I annotated my SNPs with vcfannotator and I ended up with a tab delimited .txt file like the following (complete table has 50000 rows). "SYN" stands for synonymous and "NSY" for non-synonymous substitutions. I don't have ...
snp written 14 months ago by paraskevopou20 • updated 12 months ago by Biostar ♦♦ 20
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pulling out contigs that blast to a non-relevant species from xml files
... Hi people!! I used Blast2Go in order to generate a species distribution chart (xml files used as an input to Blast2Go where generated with blast as an -outfmt5 flag). Within this list I found lots of hit (200) that blast to a non-relevant organism (plant). It seems a kind of contamination. Is ...
blast2go blast written 14 months ago by paraskevopou20 • updated 14 months ago by lakhujanivijay4.4k
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Comment: C: Select a subset of variants from a larger vcf file
... Thanks a lot. the bcftools filter command with the -R option worked perfectly. ...
written 16 months ago by paraskevopou20
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Comment: C: Extract columns from a vcf file using identifiers from a second file
... Thanks a lot. The encoding was the problem. ...
written 16 months ago by paraskevopou20
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Comment: C: Extract columns from a vcf file using identifiers from a second file
... Thanks a lot. The problem was solved. ...
written 16 months ago by paraskevopou20
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Comment: C: Extract columns from a vcf file using identifiers from a second file
... I am so sorry for this. Here is a link with the original files https://drive.google.com/open?id=1nWRK531_Mf39REjq8TcC3aQR0X8AP0aQ ...
written 16 months ago by paraskevopou20

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Popular Question 9 months ago, created a question with more than 1,000 views. For Select a subset of variants from a larger vcf file

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