User: mrodrigues.fernanda

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40
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United States / Saint Louis / Washington University in Saint Louis
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1 month ago
Joined:
5 years, 2 months ago
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Posts by mrodrigues.fernanda

<prev • 24 results • page 1 of 3 • next >
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Comment: C: InterVar and Varsome discrepancies in ACMG classification
... Please check out our automated tool for clinical characterization of germline variants following ACMG guidelines: https://github.com/ding-lab/CharGer Fernanda Martins Rodrigues | Washington University in St. Louis | Ding Lab ...
written 10 weeks ago by mrodrigues.fernanda40
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Comment: C: CrossMap VCF liftover (GRCh37 > GRCh38): END info field for indel calls not lift
... Thank you for your response, Brice! Yes, for indels called by pindel, the stop coordinate for the variant is added to the INFO field. Because that is not lifted over, it was causing issues when running the converted VCF through tools like Gatk's VariantEval. What you suggested sounds like a feasibl ...
written 4 months ago by mrodrigues.fernanda40
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Comment: C: CrossMap VCF liftover (GRCh37 > GRCh38): END info field for indel calls not lift
... I have downloaded the chain file appropriate for my case directly from the CrossMap website. I see your point, but I don't think that is the problem, since the problem is observed in all indel calls where an END field is present in the INFO field. The END field is never converted, only the variant p ...
written 4 months ago by mrodrigues.fernanda40
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CrossMap VCF liftover (GRCh37 > GRCh38): END info field for indel calls not lifted over
... Dear list, I have used CrossMap to lift over vcf files from GRCh37 coordinates to GRCh38. Here is the command: python CrossMap-0.2.8/bin/CrossMap.py vcf GRCh37_to_GRCh38.chain.gz sample1520.vcf.gz Homo_sapiens.GRCh38.dna.primary_assembly.fa sample1520.N.grch38.vcf I noticed that for some of m ...
crossmap liftover written 4 months ago by mrodrigues.fernanda40 • updated 4 months ago by Brice Sarver3.3k
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Using SVA with RRBS data
... Hello I have seen a lot of posts with this question, but have not found an answer to this. I am analyzing my RRBS data with methylKit, and I can see in my PCA plots that there are some batch effects. Is there a way to use SVA to estimate surrogate variables from methylation data? If yes, how to do ...
rrbs; sva batcheffects written 2.9 years ago by mrodrigues.fernanda40
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Answer: A: R encountered fatal error when using processBismarkAln in methylKit
... So that did not work either.Thank you for all your help though, Philipp! The solution I found for the problem was to use the cytosineReport.txt file generated by bismark. However that needs extra processing for loading into methylkit too. If anyone runs through the same problem: Run the bismark_met ...
written 2.9 years ago by mrodrigues.fernanda40
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Comment: C: R encountered fatal error when using processBismarkAln in methylKit
... Hi! Thank you for your input. Because I uses the Ovation RRBS kit from NuGen for library construction, it is recommended to use their customized nudup.py script after alignment to remove duplicates. Would you have any insights on how to fix the file? I am very new to this. Any help is appreciated. ...
written 2.9 years ago by mrodrigues.fernanda40
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Comment: C: R encountered fatal error when using processBismarkAln in methylKit
... Hi! When R crashed, it just outputted: 'R encountered a fatal errow. Session must be terminated'. I read somewhere that loading library(Rcpp) before running processBismarkAln could help, but now R is outputting the following: rsession(53014,0x7fff78526300) malloc: *** mach_vm_map(size=803107974150 ...
written 2.9 years ago by mrodrigues.fernanda40
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R encountered fatal error when using processBismarkAln in methylKit
... Hi I am attempting to use methylkit to analyse my RRBS data but cannot seem to be able to import my files. I have .bam files generated from bismark. I read I can use function processBismarkAln to read these kind of files into methylkit, but R encounters a fatal error when I try. Here is my code: ...
methylkit written 2.9 years ago by mrodrigues.fernanda40 • updated 5 months ago by ritarebollo70
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Comment: C: Question about RRBS mapping efficiency
... Devon, just a follow up on this thread. Is a mapping efficiency between 35% and 45% too low for bovine? ...
written 2.9 years ago by mrodrigues.fernanda40

Latest awards to mrodrigues.fernanda

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