User: clear.choi

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clear.choi30
Reputation:
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New User
Location:
United States
Last seen:
1 week, 1 day ago
Joined:
2 years, 3 months ago
Email:
c*********@gmail.com

Posts by clear.choi

<prev • 25 results • page 1 of 3 • next >
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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 15 days 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 15 days ago by clear.choi30
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BLAST Search to get original sequences or find fully amplified segment.
... Hello All, I set up BLAST Search program to making auto typing program. I have one question "How to bring original sequences" from output file. For example, /shared/MiSeq/BLAST/ncbi-blast-2.2.29+/bin/blastn -num_alignments 500 -word_size 50 -db ./test -query ./test.fasta -out ./test.out -ou ...
alignment hla blast dna written 15 days 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 8 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 8 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 11 months ago by clear.choi30 • updated 11 months ago by Pierre Lindenbaum88k
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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 13 months ago by clear.choi30 • updated 13 months ago by Tej Sowpati210
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Comment: C: Extract Fastq file from BAM File by reference name using samtools.
... Thank you :) ...
written 13 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 13 months ago by clear.choi30 • updated 13 months ago by Matt Shirley6.8k
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Comment: C: Extract Bamfile using samtools
... awesome :) Thank you! I ...
written 13 months ago by clear.choi30

Latest awards to clear.choi

Popular Question 14 days ago, created a question with more than 1,000 views. For How to calculate my own phred quality score
Popular Question 8 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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