User: blazer9131

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blazer913110
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New User
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United States
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2 months, 3 weeks ago
Joined:
5 years, 5 months ago
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Posts by blazer9131

<prev • 8 results • page 1 of 1 • next >
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What is the "-201", "-202", "-203", etc. suffix in Ensembl transcript names?
... I can't seem to figure out what the -201 ending for many transcript names seems to signify. Can someone point to where this is defined? Thanks! ...
ensembl written 7 months ago by blazer913110 • updated 7 months ago by Emily_Ensembl20k
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Comment: C: CollectHsMetrics base coverage output has overlapping targets
... Hi Fin, I am using picard 2.17.11, here is what's being sent: java -Xmx10g -jar picard_2.17.11.jar CollectHsMetrics I=${bam} O=${exp}.mq0.HSmetrics.txt BAIT_INTERVALS=$baits TARGET_INTERVALS=$targets REFERENCE_SEQUENCE=Homo_sapiens_assembly19.fasta PER_TARGET_COVERAGE=${exp}.mq0.target.covg TM ...
written 13 months ago by blazer913110
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CollectHsMetrics base coverage output has overlapping targets
... I am trying to get base coverage information, and am using the `--PER_BASE_COVERAGE` output to get a text file of base level coverage. However, some of my targets are being grouped together. In the targets file, these are separated by one base as such: 12 12258595 12258695 + ...
picard coverage written 13 months ago by blazer913110 • updated 11 months ago by Biostar ♦♦ 20
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Comment: C: DeconstructSigs - Multiple sample size(~90 samples)
... Hi VHahaut, using this method I have a dataframe of my samples. However when I try to do `sapply(ids, function(x) makePie(x, sub = x)` it gives me an error saying `Error in `[[.default`(sigs.output, "weights") : subscript out of bounds `. Any way I should be processing this data? ...
written 24 months ago by blazer913110
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Best Clustering Algorithms for Mutation Data?
... Hey ya'll. I have a project with about 50-60 different samples with exome sequencing data. I have genotyped these samples and there are ~150 genes which have different levels of mutation ranging from missense, nonsense, indels, amplification, deletion, etc. I tiered them in terms of biological sign ...
R written 2.3 years ago by blazer913110
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Comment: C: Annotate Ref/Alt for a list of rsIDs?
... It's roughly 600k IDs. And yes, human. ...
written 2.6 years ago by blazer913110
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Annotate Ref/Alt for a list of rsIDs?
... Hi, I have a large list of rsIDs from dbSNP. I would like to get the ref/alt for each of the snps. What would be the best way of handling this? It's a VCF containing position and dbSNP id, but no ref/alt columns. Thanks. ...
dbsnp snp written 2.6 years ago by blazer913110
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Obtaining contig stats from Velvet+Oases De Novo Assembly
... Hey all, Here's a laydown of my information. We sequenced a transcriptome. The company returned to us 4 different reads of that same transcriptome. We ran FastQC and trimmed all 4 paired reads individually. We had some contamination issues, so we ran DeconSeq on all 4 reads. We ran through the v ...
de novo assembly oases velvet written 5.4 years ago by blazer913110 • updated 5.4 years ago by Istvan Albert ♦♦ 83k

Latest awards to blazer9131

Popular Question 12 months ago, created a question with more than 1,000 views. For Annotate Ref/Alt for a list of rsIDs?
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Obtaining contig stats from Velvet+Oases De Novo Assembly

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