User: Biojl

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Biojl1.6k
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Posts by Biojl

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Comment: C: Download cdna sequences from OMA
... Thanks you very much! ...
written 24 days ago by Biojl1.6k
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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 24 days ago by Biojl1.6k
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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 25 days ago by Biojl1.6k
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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 25 days ago by Biojl1.6k • updated 24 days ago by adrian.altenhoff440
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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 6 months 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 6 months 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 7 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 7 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 7 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 7 months ago by Biojl1.6k

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