User: Marina Manrique

gravatar for Marina Manrique
Marina Manrique1.3k
Reputation:
1,260
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Trusted
Location:
Granada
Twitter:
marina_manrique
Last seen:
2 years, 6 months ago
Joined:
6 years, 9 months ago
Email:
m********@era7.com

Computational biologist. I like Bacterial Genomics, NGS and human pathogens.

And I work at Oh no sequences! (www.ohnosequences.com) group at Era7 Bioinformatics (www.era7bioinformatics.com)

You can follow me here twitter.com/marina_manrique

Posts by Marina Manrique

<prev • 92 results • page 1 of 10 • next >
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Comment: C: Are There Any Caveats When Creating A Maf File For Music?
... Hi Cyriac, I've bee using your script vcf2maf https://github.com/ckandoth/vcf2maf to get the MAF for working in Music. I could annotate it with VEP easily. My question is, how do I add the columns transcript_name amino_acid_change and c_position to it? Thanks a lot! ...
written 2.6 years ago by Marina Manrique1.3k
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Issue converting VCF to MAF using snpEff annotations
... Hi there! I'm trying to convert my VCF to MAF using snpEff for the annotations but I'm getting these errors (I'm copying just a set of them but I'm getting the same errors for every variant called in the VCF)   Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 772, < ...
maf vcf snpeff vcf2maf written 2.7 years ago by Marina Manrique1.3k • updated 15 months ago by Biostar ♦♦ 20
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Comment: C: is needed info (BAM and MAF) files for normal tissues in MUSIC?
... Thanks a lot Cyriac for the quick reply.  Cheers! marina ...
written 2.7 years ago by Marina Manrique1.3k
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is needed info (BAM and MAF) files for normal tissues in MUSIC?
... Hi there! I'm thinking about using MUSIC on a set of cancer samples but I don't have data for normal tissue. Could I use MUSIC with info of only tumor tissues? Thanks, Marina ...
maf bam music written 2.7 years ago by Marina Manrique1.3k • updated 14 months ago by hengtaofly0
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Answer: A: Vdb Field In Samtools
... A brief description of all the flags present in the INFO and FORMAT fields of the VCF file can be found in the first lines of the file (which start by ##) ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref- ...
written 4.5 years ago by Marina Manrique1.3k
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Comment: C: Prokaryotic Rnaseq Analysis-The Basics
... Tablet (http://bioinf.scri.ac.uk/tablet/) is also a good option to visualize aligned data (just need your BAM indexed) ...
written 5.4 years ago by Marina Manrique1.3k
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Answer: A: Prokaryotic Rnaseq Analysis-The Basics
... Have you considered using the Tophat-Cufflinks-Cuffdiff pipeline?, you would get what you're looking for (I guess) but avoiding the step 3 and 4 This 'pipeline' is specially designed for eukaryotic transcriptomes (since it's oriented to detect isoforms and alternative splicing events) but I think it ...
written 5.4 years ago by Marina Manrique1.3k
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Comment: C: Analysis With Cufflinks (Cuffdiff) Of Genes With No Gene Expression In One Of Th
... Thanks @David for your opinion. I completely agree with you that these genes should not be dumped and that they need special analysis. Unfortunately we don't have replicates so I'm afraid we would have to analyze each gene one by one ...
written 5.5 years ago by Marina Manrique1.3k
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Analysis With Cufflinks (Cuffdiff) Of Genes With No Gene Expression In One Of The Samples.
... Hi all, I'm using Cufflinks-Cuffdiff to get the differentially expressed genes in two samples, the thing is for some genes where their expression level in one of the two samples is 0 I get extreme (weird) values of the log2(fold change) (I guess as a result of either dividing by 0 or calculating th ...
gene cufflinks cuffdiff written 5.5 years ago by Marina Manrique1.3k • updated 5.5 years ago by David Quigley10k
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Comment: C: David For Rnaseq Data
... Thanks a lot for the comments! ...
written 5.7 years ago by Marina Manrique1.3k

Latest awards to Marina Manrique

Popular Question 2.6 years ago, created a question with more than 1,000 views. For What Is Your Experience With Igenomes?
Appreciated 3.3 years ago, created a post with more than 5 votes. For A: Links To Good Next Gen Sequence Analysis Training Courses And Centres
Great Question 3.3 years ago, created a question with more than 5,000 views. For How To Retrieve A .Fastaq File From Sra Using Wget? (And Not Aspera)
Good Question 3.3 years ago, asked a question that was upvoted at least 5 times. For How To Retrieve A .Fastaq File From Sra Using Wget? (And Not Aspera)
Student 3.3 years ago, asked a question with at least 3 up-votes. For Equivalent Blast And Blast+ Commands
Appreciated 3.7 years ago, created a post with more than 5 votes. For A: Links To Good Next Gen Sequence Analysis Training Courses And Centres
Appreciated 3.7 years ago, created a post with more than 5 votes. For A: I Need A List Of Bayesian Snp/Genotype Callers
Appreciated 3.7 years ago, created a post with more than 5 votes. For A: Clustering Go Terms?
Appreciated 3.7 years ago, created a post with more than 5 votes. For A: Is There A Free Alternative To Ingenuity Pathway Analysis?
Appreciated 3.7 years ago, created a post with more than 5 votes. For A: Bacterial Annotation Pipeline
Appreciated 3.7 years ago, created a post with more than 5 votes. For Bacterial Diversity Identification With Normalized Libraries?
Good Answer 3.7 years ago, created an answer that was upvoted at least 5 times. For A: Links To Good Next Gen Sequence Analysis Training Courses And Centres
Good Answer 3.7 years ago, created an answer that was upvoted at least 5 times. For A: Clustering Go Terms?
Good Answer 3.7 years ago, created an answer that was upvoted at least 5 times. For A: Is There A Free Alternative To Ingenuity Pathway Analysis?
Good Answer 3.7 years ago, created an answer that was upvoted at least 5 times. For A: Bacterial Annotation Pipeline
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Equivalent Blast And Blast+ Commands
Popular Question 3.7 years ago, created a question with more than 1,000 views. For David For Rnaseq Data
Popular Question 3.7 years ago, created a question with more than 1,000 views. For How To Retrieve A .Fastaq File From Sra Using Wget? (And Not Aspera)
Popular Question 3.7 years ago, created a question with more than 1,000 views. For [Errno 8] Exec Format Error Using Tophat 1.3.1
Guru 3.7 years ago, received more than 100 upvotes.
Voter 3.7 years ago, voted more than 100 times.
Supporter 3.7 years ago, voted at least 25 times.
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Where To Get Downloadable Annotated Microbial Transcriptome Sequences?
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Links To Good Next Gen Sequence Analysis Training Courses And Centres

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