User: mariamcurbelo2061

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Posts by mariamcurbelo2061

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Natural Selection in cancer genomes
... Hello...I´m kind of a newbie in bioinformatics and cancer biology in general. Many papers use the dn/ds method to test for natural selection in cancer genomes, and I have also used it, kind of following the notion of: If they do it they must have a reason. But now I face myself to the question of wh ...
dn/ds cancer natural selection written 3 months ago by mariamcurbelo20610
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Answer: A: Extracting MAF for a list of SNPs
... Hi, I'm a newbie in bioinformatics, so sorry if my answer is not the most complete one. I found myself with the similar problem of extracting info from a MAF. I solved it with python panda package. An example will be: maf_file = panda.read_table("PATH") filter_maf_file = maf_file.query('na ...
written 4 months ago by mariamcurbelo20610
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Comment: C: In MAF files, does c_position is equivalent to cDNA_positions?
... The mafs were obtained from here https://www.synapse.org/#!Synapse:syn1729383.2 (I'm currently working with BRCA) I'll add a sample to the question ...
written 5 months ago by mariamcurbelo20610
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In MAF files, does c_position is equivalent to cDNA_positions?
... Hello I'm working with TCGA maf for BRCA, (version 37 of the genome). In the GDC documentation about mafs https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/ they mention a field called cDNA_positions, all I can find in my maf is c_position. Is it the same? Thanks in advance EDIT: This is a s ...
maf genome cdna gdc written 5 months ago by mariamcurbelo20610
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Comment: C: Sliding Window Ka/Ks (Dn/Ds) Analysis Via Python?
... Hi, 5 years later I have the exact same problem...did you figure it out? Thanks in advance ...
written 6 months ago by mariamcurbelo20610
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How to generate a mutated DNA sequence?
... Hi, I'm a newbie in bioinformatics, I just want to know how to build an accurate (not random) mutated sequence of a given gene. With the mutations coming from .mafs provided by TCGA.(Just taking into account point mutations). Thanks in advance I've been reading a lot but the more I read the less I ...
sequence mutations written 6 months ago by mariamcurbelo20610 • updated 6 months ago by Biostar ♦♦ 20
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What does TCGA uses a a reference for making snp annotation?
... Hi, as it may seem for my question I'm a newbie at dealing with all the too many databases for sequences. The situation: I have some .maf with mutations of a given cancer, let's say breast cancer, and a given gene, TP53. The .maf clearly says where the mutations start and end. (I'm just interested ...
genome tcga refseq snp written 6 months ago by mariamcurbelo20610 • updated 6 months ago by i.sudbery5.3k
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Answer: A: Calculate Average Dn And Ds For Gene Families
... Using PALM on python worked for me. It generates a dictionary, and you can access to all the variables, including of course dn and ds separately ...
written 8 months ago by mariamcurbelo20610
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Comment: C: Error in module A of TCGA assembler
... And this is what I get on the console > source("Module_A.R") > source("Module_B.R") > sPath1 <- "./QuickStartExample/Part1_DownloadedData" > sPath2 <- "./QuickStartExample/Part2_BasicDataProcessingResult" > sPath3 <- "./QuickStartExample/Part3_Advance ...
written 8 months ago by mariamcurbelo20610
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Comment: C: Error in module A of TCGA assembler
... source("Module_A.R") source("Module_B.R") sPath1 <- "./QuickStartExample/Part1_DownloadedData" sPath2 <- "./QuickStartExample/Part2_BasicDataProcessingResult" sPath3 <- "./QuickStartExample/Part3_AdvancedDataProcessingResult" sCancer <- "BRCA" vPatientID <- ...
written 8 months ago by mariamcurbelo20610

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