User: clear.choi

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clear.choi30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
2 weeks, 2 days ago
Joined:
3 years ago
Email:
c*********@gmail.com

Posts by clear.choi

<prev • 35 results • page 1 of 4 • next >
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Best Alignment tool of Denovo assembly Results.
... I have Denovo Assembly sequence from PacBio sequence. It is around 2.9 GB size of sequences. I'd like to know what is best alignment tool to analyze this data. I am usually using this "blasr" to align HG19 to Sub reads. However, When I align HG19 to Denovo assembly results, It throwing the error ...
assembly sequence snp alignment written 19 days ago by clear.choi30 • updated 15 days ago by colindaven340
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Comment: C: HG19 Annotation download with Gene Names.
... Just for other people information, They need to download "genePredToBed" in http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64 location. ...
written 4 weeks ago by clear.choi30
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Comment: C: HG19 Annotation download with Gene Names.
... wow!! this is working perfectly. Thank you so much! ...
written 4 weeks ago by clear.choi30
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Comment: C: HG19 Annotation download with Gene Names.
... Thank you! I will look into it. ...
written 4 weeks ago by clear.choi30
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Comment: C: HG19 Annotation download with Gene Names.
... Thank you for your reply! Please check below parameter, genome : Human, assembly: hg19, group : Genes and Gene Predictions, track : RefSeq Genes, table : refGene, output format : bed file, region : genome. ...
written 4 weeks ago by clear.choi30
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HG19 Annotation download with Gene Names.
... I'd like to download bed file (annotation) like IGV tools have, If I choose Human hg19 reference from IGV. It is automatically set all annotation tracks. I downloaded one from below location, http://genome.ucsc.edu/cgi-bin/hgTables?command=start However, Name is not exactly what I wanted. For ex ...
genome annotation hg19 bed igv written 4 weeks ago by clear.choi30 • updated 4 weeks ago by genecats.ucsc410
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Comment: C: Analyzing whole genomic sequence.
... Thank you so much for your information! yes, sequence provider has been checked sequence quality. I am running it right now! I will see how does it look like! And also Could you share with me normally how informatics team analyze de novo assembly results? ...
written 5 months ago by clear.choi30
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Comment: C: Analyzing whole genomic sequence.
... It is PacBio Platform. I'd like to study how we are analyzing de novo assembly sequence results using visualization tool. ...
written 5 months ago by clear.choi30
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Comment: C: Analyzing whole genomic sequence.
... Yes, human genome sequence that has been de novo assembled, and also Looks like there are many contigs/sequences in the sample fasta file. Thank you for suggest tool ! I'd like to see sequence using visualization tool like IGV. So I wants to see how does it looks like. Like Resequencing. ...
written 5 months ago by clear.choi30
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Analyzing whole genomic sequence.
... I am new for analyzing whole genomic sequences, I got de novo assembly results (fasta file format and around 4400 indexes). This is huge file (file size is around 3GiB) I tried to analyze this data with HG19. So I was using BWA and Blasr for alignment. but It was failed (BWA is core dump. Blasr is ...
next-gen alignment sequencing written 5 months ago by clear.choi30

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Popular Question 9 months ago, created a question with more than 1,000 views. For How to calculate my own phred quality score
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