User: clear.choi

gravatar for clear.choi
clear.choi30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
2 months, 1 week ago
Joined:
2 years, 6 months ago
Email:
c*********@gmail.com

Posts by clear.choi

<prev • 25 results • page 1 of 3 • next >
0
votes
0
answers
131
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 10 weeks 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 3 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 3 months ago by clear.choi30
0
votes
0
answers
337
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 11 months ago by clear.choi30
1
vote
0
answers
337
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 11 months ago by clear.choi30
2
votes
1
answer
691
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 14 months ago by clear.choi30 • updated 14 months ago by Pierre Lindenbaum92k
2
votes
1
answer
1.5k
views
1
answer
How to calculate my own phred quality score
... I am planning to calculate my own phred quality score. I need to share some idea how to calculate my own Q Score. I have a sequences like below,           AAAAAAAAAAAAAAAAAAAAAA         AAAAAAAAAAAAAAAAAAAAAA         AAAAAAAAAAAAAAAAAAAAAA         AAAAAAAAAAAAAAAAAAAAAA         AAAAAAAAAAAAA ...
fastq qscore phred quality score quality score written 16 months ago by clear.choi30 • updated 16 months ago by Tej Sowpati230
0
votes
1
answer
684
views
1
answers
Comment: C: Extract Fastq file from BAM File by reference name using samtools.
... Thank you :) ...
written 16 months ago by clear.choi30
4
votes
1
answer
684
views
1
answer
Extract Fastq file from BAM File by reference name using samtools.
... Hello,   I am trying to understand how to use samtools, and there is a little bit confusion. I have one .BAM file which is 96 index is existed. I can extract that specific index like below samtool view -r B3 -b -o out.bam in.bam [ Ref : https://www.biostars.org/p/168386/ ] But I wonder if I w ...
bam samtools sam written 16 months ago by clear.choi30 • updated 16 months ago by Matt Shirley7.2k
0
votes
1
answer
507
views
1
answers
Comment: C: Extract Bamfile using samtools
... awesome :) Thank you! I ...
written 17 months ago by clear.choi30

Latest awards to clear.choi

Popular Question 3 months ago, created a question with more than 1,000 views. For How to calculate my own phred quality score
Popular Question 11 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: 1530 users visited in the last hour