User: clear.choi

gravatar for clear.choi
clear.choi30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
9 months, 3 weeks ago
Joined:
3 years, 9 months ago
Email:
c*********@gmail.com

Posts by clear.choi

<prev • 35 results • page 1 of 4 • next >
1
vote
1
answer
500
views
5 follow
1
answer
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 9 months ago by clear.choi30 • updated 9 months ago by colindaven740
0
votes
1
answer
1.1k
views
1
answers
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 10 months ago by clear.choi30
0
votes
1
answer
1.1k
views
1
answers
Comment: C: HG19 Annotation download with Gene Names.
... wow!! this is working perfectly. Thank you so much! ...
written 10 months ago by clear.choi30
0
votes
1
answer
1.1k
views
1
answers
Comment: C: HG19 Annotation download with Gene Names.
... Thank you! I will look into it. ...
written 10 months ago by clear.choi30
0
votes
1
answer
1.1k
views
1
answers
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 10 months ago by clear.choi30
2
votes
1
answer
1.1k
views
1
answer
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 10 months ago by clear.choi30 • updated 10 months ago by genecats.ucsc500
0
votes
0
answers
474
views
0
answers
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 14 months ago by clear.choi30
0
votes
0
answers
474
views
0
answers
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 14 months ago by clear.choi30
0
votes
0
answers
474
views
0
answers
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 14 months ago by clear.choi30
2
votes
0
answers
474
views
0
answers
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 14 months ago by clear.choi30

Latest awards to clear.choi

Popular Question 18 months ago, created a question with more than 1,000 views. For How to calculate my own phred quality score
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Mismatch during Merge Paired-End Reads in FLASH Algorithm

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 965 users visited in the last hour