User: little_more

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Posts by little_more

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How to get a strain name if I know only an assembly ID?
... Suppose I have a tree with assembly IDs of different E.coli strains in it (all from NCBI). Is there any common way to replace each assembly ID with the corresponding strain name? I tried using BioPython (efetch) but it raises an error. ...
assembly written 22 days ago by little_more0 • updated 22 days ago by vkkodali450
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Comment: C: How to get fasta sequences for CDS if I have proteins IDs?
... Thank you! But is it possible to use the command for > 500 IDs? Documentations says 'a comma-delimited list of UIDs may be provided... but if more than about 200 UIDs are to be provided, the request should be made using the HTTP POST method'. ...
written 4 weeks ago by little_more0
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Comment: C: How to get fasta sequences for CDS if I have proteins IDs?
... IDs are from different genomes. In fact, I have a table with protein IDs: group1 group2 group3 group4 ... bac1 ID1 ID2 ID3 ID4 bac2 ID5 ID6 ID7 ID8 bac3 ID9 ID10 ID11 ID12 ... and I need ...
written 4 weeks ago by little_more0
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Comment: C: How to get fasta sequences for CDS if I have proteins IDs?
... Oh, my bad. All IDs are from GenBank *Escherichia* genome assemblies (.faa files). For example, AAN78512.1, BAB33431.1, BAB33432.1. P.S. I know that I can simply go to NCBI and get CDS for each protein manually but the question is how to do this for a large number of ID groups. I've heard somethin ...
written 4 weeks ago by little_more0
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How to get fasta sequences for CDS if I have proteins IDs?
... I have a large table where each column contains protein IDs of a particular group of orthologs. How do I map these protein IDs to gene IDs and then get a file with fasta sequences of all genes for each column? ...
gene sequence written 5 weeks ago by little_more0 • updated 4 weeks ago by h.mon21k
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Comment: C: Correlation of expression and compartmentalization
... Well, thank you for the link, but the question was actually about the way to estimate correlation. Moreover, how to use a .bigwig file for that? ...
written 8 months ago by little_more0
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Comment: C: Correlation of expression and compartmentalization
... k562, for example. I'd like to compute Spearman correlation as in the Liberman-aiden paper. ...
written 8 months ago by little_more0
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Correlation of expression and compartmentalization
... Hello everyone! Suppose I defined two compartments 1 and 2 and I have a number of vectors with probabilities of a chromosomal locus to be in a compartment 1 for each chromosome. How can I estimate the Spearman correlation between expression and compartmentalization for each chromosome for the known ...
R rna-seq written 8 months ago by little_more0 • updated 8 months ago by Sean Davis25k

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