User: Biojl

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Biojl1.6k
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Posts by Biojl

<prev • 195 results • page 1 of 20 • next >
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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 10 weeks ago by Biojl1.6k
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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 11 weeks ago by Biojl1.6k
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Comment: C: options for RNA polymerase II-chipseq data using macs2 callpeak
... What did you do in the end? ...
written 3 months ago by Biojl1.6k
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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 3 months ago by Biojl1.6k
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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 3 months ago by Biojl1.6k
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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 3 months ago by Biojl1.6k
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Answer: A: How to visualize a tree with ancestral state information
... If you want to plot a tree with annotation in an automated way your best bet is ETE: http://etetoolkit.org/ You can do almost anything you want with a tree programmaticly. Is python based. ...
written 4 months ago by Biojl1.6k
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Comment: C: How to deal with one-to-many orthologies in PAML
... In general people focus on one-to-one orthologs (and skips one-to-many or many-to-many) in their analyses precisely to avoid this problem. ...
written 4 months ago by Biojl1.6k
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Comment: C: parse xml proteinpredict files
... Wow, definitely is worth it to learn how to use XSL!! Just one question about the code, in which part you select the info for the first column (ADRB2_HUMAN)? I don't understand this language yet. ...
written 7 months ago by Biojl1.6k
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Comment: C: parse xml proteinpredict files
... Is not there, is a made up protein ID. The protein ID is usually in the file name. ...
written 7 months ago by Biojl1.6k

Latest awards to Biojl

Scholar 3 months ago, created an answer that has been accepted. For A: Long Motif Predicted by MEME SUITE
Popular Question 7 months ago, created a question with more than 1,000 views. For convert GFF3 files from one genome version to another (Drosophila)
Popular Question 7 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 11 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 11 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 11 months ago, created a question with more than 1,000 views. For Obtain conservation (or % ident) in a multiple sequence alignment
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Biostar Ads Are Here! Showcase Your Accomplishments To The World!
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Status Quo: Trinity Vs Oases
Scholar 15 months ago, created an answer that has been accepted. For A: Long Motif Predicted by MEME SUITE
Popular Question 16 months ago, created a question with more than 1,000 views. For Obtain conservation (or % ident) in a multiple sequence alignment
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Status Quo: Trinity Vs Oases
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Automatic Data Extraction From Timetree
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Biopython And Codeml Module. Error.
Popular Question 2.5 years ago, created a question with more than 1,000 views. For How To Parallelize Codeml With Python
Popular Question 2.5 years ago, created a question with more than 1,000 views. For How To Parallelize Codeml With Python
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Automatic Data Extraction From Timetree
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Automatic Data Extraction From Timetree
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Where To Get A Mammalian Phylogenetic Tree With Branch Distances.
Popular Question 3.3 years ago, created a question with more than 1,000 views. For How To Parallelize Codeml With Python
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Where To Get A Mammalian Phylogenetic Tree With Branch Distances.
Popular Question 4.3 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 Status Quo: Trinity Vs Oases
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