User: christacaggiano

Reputation:
20
Status:
New User
Location:
UCSF
Last seen:
3 months ago
Joined:
2 years, 3 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 • 16 results • page 1 of 2 • next >
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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 8 months ago by christacaggiano20
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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 9 months ago by christacaggiano20 • updated 9 months ago by finswimmer11k
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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 11 months ago by christacaggiano20
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Comment: C: test dataset for MinIon algorithm development
... Yes. Not looking for fastqs that are already base-called ...
written 11 months ago by christacaggiano20
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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 11 months ago by christacaggiano20 • updated 11 months ago by WouterDeCoster37k
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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 13 months ago by christacaggiano20
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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 15 months ago by christacaggiano20 • updated 15 months ago by igor7.4k
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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 17 months ago by christacaggiano20
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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 19 months ago by christacaggiano20
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simulating variants with specific frequency using GATK
... Hi, Given a VCF file that I want to use GATK SimulateReadsForVariants to generate simulated data containing those variants (mostly indels) is there a way to specify that the variants be generated at a specific allele frequency? This is the package I hope to use: https://software.broadinstitute.or ...
vcf gatk written 21 months ago by christacaggiano20 • updated 20 months ago by Biostar ♦♦ 20

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Popular Question 17 months ago, created a question with more than 1,000 views. For Peak center for ATAC-seq data
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