User: clear.choi

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clear.choi30
Reputation:
30
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New User
Location:
United States
Last seen:
1 month, 1 week ago
Joined:
2 years, 5 months ago
Email:
c*********@gmail.com

Posts by clear.choi

<prev • 25 results • page 1 of 3 • next >
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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 6 weeks ago by clear.choi30
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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 11 weeks ago by clear.choi30
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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 11 weeks ago by clear.choi30
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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 10 months ago by clear.choi30
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[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 10 months ago by clear.choi30
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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 13 months ago by clear.choi30 • updated 13 months ago by Pierre Lindenbaum91k
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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 15 months ago by clear.choi30 • updated 15 months ago by Tej Sowpati230
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Comment: C: Extract Fastq file from BAM File by reference name using samtools.
... Thank you :) ...
written 15 months ago by clear.choi30
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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 15 months ago by clear.choi30 • updated 15 months ago by Matt Shirley7.1k
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Comment: C: Extract Bamfile using samtools
... awesome :) Thank you! I ...
written 15 months ago by clear.choi30

Latest awards to clear.choi

Popular Question 11 weeks ago, created a question with more than 1,000 views. For How to calculate my own phred quality score
Popular Question 10 months ago, created a question with more than 1,000 views. For Mismatch during Merge Paired-End Reads in FLASH Algorithm

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