User: clear.choi

gravatar for clear.choi
clear.choi30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
3 weeks, 5 days ago
Joined:
2 years, 8 months ago
Email:
c*********@gmail.com

Posts by clear.choi

<prev • 29 results • page 1 of 3 • next >
0
votes
0
answers
155
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 6 weeks ago by clear.choi30
0
votes
0
answers
155
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 6 weeks ago by clear.choi30
0
votes
0
answers
155
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 6 weeks ago by clear.choi30
2
votes
0
answers
155
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 6 weeks ago by clear.choi30
0
votes
0
answers
192
views
0
answers
IGV Allele Frequency threshold.
... Hello all , I'd like to understand of Allele frequency. If I change allele frequency threshold from 0.2 to 0.02, Color graph of bases are appear (from gray color) Does anyone clearly know what is this threshold for? Sincerely, ...
alignment bam igv written 4 months ago by clear.choi30
0
votes
0
answers
127
views
0
answers
Comment: C: BLAST Search to get original sequences or find fully amplified segment.
... I want to make sure I can distinguish It is fully amplified based on Reference sequence using Blast output without checking original sequence and raw sequence again. If It is difficult to get that information from BLAST output, at least I need to get original sequences. then I can make some calculat ...
written 5 months ago by clear.choi30
0
votes
0
answers
127
views
0
answers
Comment: C: BLAST Search to get original sequences or find fully amplified segment.
... @WouterDeCoster That is not actual sequence, It is just for example. ...
written 5 months ago by clear.choi30
0
votes
0
answers
383
views
0
answers
Comment: C: [NCBI BLAST] MAKE Limitation of BLAST Results.
... @Jenez Sorry for confusing you, Yes It is! I would like to bring only two alignment information excluding the third alignment. ...
written 13 months ago by clear.choi30
1
vote
0
answers
383
views
0
answers
[NCBI BLAST] MAKE Limitation of BLAST Results.
... Hello, I am using blast version ncbi-blast-2.2.29+. I wonder how I can make limitation of alignment information per allele For Example as below, If blast search results like below, > AI4E8.UA Length=130 Score = 99.0 bits (53), Expect = 2e-22 Identities = 53/53 (100%), Gaps ...
ncbi blast written 13 months ago by clear.choi30
2
votes
1
answer
795
views
1
answer
BLAST geneate Output SAM file , Missing aligned sequences.
... I have tried to use ncbi blast 2.3.0 version which support output sam file. I did it like below,   /program/ncbi-blast-2.3.0+/bin/blastn -db /db/class2.db -max_target_seqs 1 -outfmt 17  -query  ./S4--S4.fasta -out ./S4--S4.sam Then I got strange results that first all reference Name and Query Na ...
blast bam sam output rna-seq written 16 months ago by clear.choi30 • updated 16 months ago by Pierre Lindenbaum95k

Latest awards to clear.choi

Popular Question 5 months ago, created a question with more than 1,000 views. For How to calculate my own phred quality score
Popular Question 13 months 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: 1275 users visited in the last hour