User: christacaggiano

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50
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Trusted
Location:
UCSF
Last seen:
14 hours ago
Joined:
3 years, 8 months ago
Email:
c**************@gmail.com

A biophysicist turned bioinformatics graduate student. I am interested in computational genomics and algorithms development. 

Posts by christacaggiano

<prev • 17 results • page 1 of 2 • next >
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Finding shared genotypes between multiple VCF files
... I have several VCF files generated from WES. Some share a condition, and others could be considered controls. I want to know which SNPs are shared between the files with the condition, and not in the controls. By "shared" I mean for a given SNP, I want to know whether they share the same genotype at ...
vcf exome snp written 27 days ago by christacaggiano50 • updated 27 days ago by Pierre Lindenbaum129k
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differentially methylated bed file from encode
... I am looking to compile all the tissues profiled in the ENCODE WGBS and RRBS experiments into one matrix, and find all the differentially methylated regions, which has turned out to be a monumental amount of data. I'm looking for something similar to the roadmap fractional methylation calls found [h ...
encode methylation wgbs written 2.1 years ago by christacaggiano50
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Combining multiple bedfiles
... I have many (>100) bed files in this format file1 chr1 1 2 2 chr1 10 11 3 chr1 50 51 4 file2 chr1 1 2 10 chr1 10 11 8 chr10 2 3 8 fileN chr1 1 2 1 chr1 50 51 2 chr10 2 3 9 where the files have some sites in common, but not all of ...
bedtools bed written 2.2 years ago by christacaggiano50 • updated 11 weeks ago by Biostar ♦♦ 20
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Comment: C: test dataset for MinIon algorithm development
... Yeah I guess the fast5 files are ~500GB, I was hoping for something on <5GB just to test some ideas out ...
written 2.4 years ago by christacaggiano50
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Comment: C: test dataset for MinIon algorithm development
... Yes. Not looking for fastqs that are already base-called ...
written 2.4 years ago by christacaggiano50
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test dataset for MinIon algorithm development
... Hi, Can anyone point me to a test dataset that contains raw picoAmp data generated by the Oxford Nanopore MinIon platform? I am interested in algorithm development for this type of data but I would like to get a sense of the data before we begin sequencing on our own MinIon. My problem currently i ...
nanopore sequencing written 2.4 years ago by christacaggiano50 • updated 2.4 years ago by WouterDeCoster44k
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low mappability in single cell rna-seq data?
... Hi, Using the STAR aligner, I am getting a very low mapping percentage for my single cell RNA seq data (5-10%). A majority of my reads are being considered "too short" (>90%). My current parameters are `STAR --genomeDir --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3 --outRea ...
alignment contamination rna-seq written 2.6 years ago by christacaggiano50
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more than 28 million methylation sites?
... Hi, I am currently doing a whole genome bisulfite sequencing experiment. After running Bismark methylation caller and calculating percent methylation for each unique CpG, I am coming up with more than 46 million sites. I know that there are only 28 million sites in the genome, so I am very confuse ...
methylation bs-seq bismark cpg written 2.7 years ago by christacaggiano50 • updated 2.7 years ago by igor11k
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ENCODE methylation pipeline for command line
... Hi, Does anyone know of an implementation of the ENCODE WGBS pipeline for the command line? I am familiar with the DNAnexus implementation and this implementation, https://github.com/ENCODE-DCC/dna-me-pipeline , however, I cannot get the above to work on our lab's cluster The pipeline I am refer ...
encode methylation wgbs written 2.9 years ago by christacaggiano50
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Answer: A: Soft-clipping of reads in Amplicon-sequenced data
... Also keep in mind that soft clipping can happen when regions with insertions and deletions occur and your software is unable to map them to the genome properly. If you're planning on calling indels later, especially with software that isn't clipping-aware this could affect how well you call them. ...
written 3.0 years ago by christacaggiano50

Latest awards to christacaggiano

Popular Question 15 months ago, created a question with more than 1,000 views. For need advice on installing ZINBA on new version of R
Popular Question 15 months ago, created a question with more than 1,000 views. For Combining multiple bedfiles
Popular Question 15 months ago, created a question with more than 1,000 views. For low mappability in single cell rna-seq data?
Popular Question 20 months ago, created a question with more than 1,000 views. For Peak center for ATAC-seq data
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Peak center for ATAC-seq data
Autobiographer 3.4 years ago, has more than 80 characters in the information field of the user's profile.

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