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User: Biojl

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Biojl • 1.6k
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Biologist

https://scholar.google.es/citations?user=rwqsvWYAAAAJ&hl=es

 

Posts by Biojl

<prev • 199 results • page 1 of 20 • next >
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Comment: C: Download cdna sequences from OMA
... Thanks you very much! ...
written 12 weeks ago by Biojl • 1.6k
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Comment: C: Download cdna sequences from OMA
... There is not. I don't want to download a 2.4Gb compressed file and parse it every time I want the cDNA of a bunch of orthologs. There is an option to download all the ortholog protein sequences when you search a particular protein. I was looking for the same with cDNA. ...
written 12 weeks ago by Biojl • 1.6k
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Comment: C: Download cdna sequences from OMA
... Yes, this is what I did, but it would be nice to have a bulk download of cDNA for selected sequences, just as there is for proteins ...
written 12 weeks ago by Biojl • 1.6k
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Download cdna sequences from OMA
... Hi, I am trying to obtain the cdna sequences for orthologs groups. There is a button for *Download: Fasta* but apparently it only works for the protein sequences. Does anybody know if there is a way to download them in bulk as opposed to download every single sequence individually? ...
orthologs oma written 12 weeks ago by Biojl • 1.6k • updated 12 weeks ago by adrian.altenhoff • 450
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Comment: C: calculating dn/ds from codeml output
... Are your running codeml through biopython? Is relatively easy to parse the output: https://github.com/biopython/biopython/blob/master/Bio/Phylo/PAML/codeml.py ...
written 8 months ago by Biojl • 1.6k
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Answer: A: Find transcription factors that may regulate list of genes
... What about calculating a Log odds ratio (LOR) using a pre-defined area around your genes of interest. Count the number of TFBS in those regions and compare it against the whole genome and/or other genes not related to the modules you want to test, to correct for the effect of having genes around you ...
written 8 months ago by Biojl • 1.6k
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Comment: C: options for RNA polymerase II-chipseq data using macs2 callpeak
... What did you do in the end? ...
written 9 months ago by Biojl • 1.6k
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Comment: C: Extract columns from a vcf file using identifiers from a second file
... You are working with MAC right? You have a weird file structure, it has \r (mac) and \n (unix). To fix them you have to remove the \r: [jl@gaia drive-download-20180509T103851Z-001]$ tr -d '\r' < file1.txt > unixfile1.txt [jl@gaia drive-download-20180509T103851Z-001]$ tr -d '\r' < ...
written 9 months ago by Biojl • 1.6k
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Comment: C: Extract columns from a vcf file using identifiers from a second file
... You should always provide the original files so people can run tests. Also this tr command you are using is removing all tabs preceded by a space... which is not useful at all. If your separating character is one space just try `join -t $' ' <(sort -k1,1 file1) <(sort -k1,1 file2)` ...
written 9 months ago by Biojl • 1.6k
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Answer: A: Extract columns from a vcf file using identifiers from a second file
... Assuming that the separating character is '\t' I think that join is faster for larger files. In order to use the join command the files have to be sorted by the common field (in this case in both files is the first field, but it could be different). join -t $'\t' <(sort -k1,1 file1) <(sor ...
written 9 months ago by Biojl • 1.6k

Latest awards to Biojl

Appreciated 18 days ago, created a post with more than 5 votes. For A: How Has Bioinformatics Improved Over Time?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How Has Bioinformatics Improved Over Time?
Popular Question 3 months ago, created a question with more than 1,000 views. For Where to obtain a gene rpkm matrix for mouse (from mouse encode)
Great Question 6 months ago, created a question with more than 5,000 views. For Where To Get A Mammalian Phylogenetic Tree With Branch Distances.
Scholar 9 months ago, created an answer that has been accepted. For A: Long Motif Predicted by MEME SUITE
Popular Question 13 months ago, created a question with more than 1,000 views. For Where to obtain a gene rpkm matrix for mouse (from mouse encode)
Popular Question 13 months ago, created a question with more than 1,000 views. For convert GFF3 files from one genome version to another (Drosophila)
Popular Question 17 months ago, created a question with more than 1,000 views. For Where to obtain a gene rpkm matrix for mouse (from mouse encode)
Popular Question 17 months ago, created a question with more than 1,000 views. For Where to obtain a gene rpkm matrix for mouse (from mouse encode)
Popular Question 17 months ago, created a question with more than 1,000 views. For Obtain conservation (or % ident) in a multiple sequence alignment
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: Biostar Ads Are Here! Showcase Your Accomplishments To The World!
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Status Quo: Trinity Vs Oases
Scholar 21 months ago, created an answer that has been accepted. For A: Long Motif Predicted by MEME SUITE
Popular Question 22 months ago, created a question with more than 1,000 views. For Obtain conservation (or % ident) in a multiple sequence alignment
Popular Question 22 months ago, created a question with more than 1,000 views. For Calculate Pairwise Wilcox.Test For Several Categories And Plot Significance Into A Boxplot With Ggplot2
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Status Quo: Trinity Vs Oases
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Automatic Data Extraction From Timetree
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Biopython And Codeml Module. Error.
Popular Question 3.0 years ago, created a question with more than 1,000 views. For How To Parallelize Codeml With Python
Popular Question 3.0 years ago, created a question with more than 1,000 views. For How To Parallelize Codeml With Python
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Automatic Data Extraction From Timetree
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Automatic Data Extraction From Timetree
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Where To Get A Mammalian Phylogenetic Tree With Branch Distances.
Popular Question 3.8 years ago, created a question with more than 1,000 views. For How To Parallelize Codeml With Python
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Calculate Pairwise Wilcox.Test For Several Categories And Plot Significance Into A Boxplot With Ggplot2
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