User: christacaggiano
christacaggiano • 20
- Reputation:
- 20
- Status:
- New User
- Location:
- UCSF
- Last seen:
- 3 days, 5 hours ago
- Joined:
- 1 year, 7 months ago
- Email:
- c**************@gmail.com
A biophysicist turned bioinformatics graduate student. I am interested in computational genomics and algorithms development.
Posts by christacaggiano
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4
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... 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 ...
written 12 days ago by
christacaggiano • 20
• updated
12 days ago by
finswimmer ♦ 2.8k
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... Yeah I guess the fast5 files are ~500GB, I was hoping for something on <5GB just to test some ideas out ...
written 11 weeks ago by
christacaggiano • 20
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... Yes. Not looking for fastqs that are already base-called ...
written 11 weeks ago by
christacaggiano • 20
1
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... 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 ...
written 11 weeks ago by
christacaggiano • 20
• updated
11 weeks ago by
WouterDeCoster ♦ 29k
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... 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 ...
written 5 months ago by
christacaggiano • 20
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... 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 ...
written 6 months ago by
christacaggiano • 20
• updated
6 months ago by
igor ♦ 6.2k
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... 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 ...
written 9 months ago by
christacaggiano • 20
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3
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... 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 10 months ago by
christacaggiano • 20
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... 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 ...
written 12 months ago by
christacaggiano • 20
• updated
11 months ago by
Biostar ♦♦ 20
1
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522
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... I typically used homer annotatePeaks.pl to find my TSS when I was working with Atac-seq data
http://homer.ucsd.edu/homer/ngs/annotation.html
this gives you a good estimate of the distance of the peak to a TSS and the output is an excel table that can be easily made into a bedfile.
Hope this hel ...
written 12 months ago by
christacaggiano • 20
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