User: Wen.Huang

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Wen.Huang1.1k
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Posts by Wen.Huang

<prev • 56 results • page 1 of 6 • next >
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Answer: A: Fetching Genbank Entries For List Of Accession Numbers.
... two not so specific cents: 1) NCBI has a well documented but under-used collection of E-utilities you may want to try 2) Bio-perl has modules to fetch GenBank entries using different IDs. ...
written 4.3 years ago by Wen.Huang1.1k
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Answer: A: Filtering Fastq Sequences Based On Lengths
... cat your.fastq | paste - - - - | awk 'length($2) >= 21 && length($2) <= 25' | sed 's/\t/\n/g' > filtered.fastq ...
written 4.3 years ago by Wen.Huang1.1k
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Answer: A: Fastphase To Plink Format
... convert this format to plink's tped format, which is very similar to fastPHASE outputs, just a few extra columns make a tfam file with the individual ID, etc. with tped and tfam on hands, you can use plink to make various conversion if you need ...
written 4.3 years ago by Wen.Huang1.1k
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Difference Between Edit-Distance And Mismatch In Tophat
... Hi everybody, I was wondering if any body knows what is the difference between the options in tophat? -N: number of mismatches and -read-edit-dist: number of edit distance what would be the number of mismatches and edit distance respectively for a 2-bp indel? Thanks, Wen ...
tophat written 4.7 years ago by Wen.Huang1.1k • updated 4.7 years ago by Ido Tamir4.7k
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8 follow
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Converting Blast Output To Sam Format
... Hi everybody, I was wondering if there is a blast output parser that convert blast output to SAM format. There are many blast parser out there, but most for compressing results to more readable statistics. I would appreciate if anybody can point me to something that extracts the alignments. Thanks ...
sam blast parser written 4.8 years ago by Wen.Huang1.1k • updated 24 months ago by Pierre Lindenbaum95k
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Answer: A: What Do Chromosome Codes Such As 'Chr_Random' Represent?
... PLINK would not work with those chromosome numbers (only 1-22, X, Y, XY, and M work) .For these unconventional names you might be able to assign ID to them (e.g. chr_pos) and then put them on chromosome "0" (unmapped). ...
written 4.8 years ago by Wen.Huang1.1k
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Answer: A: How To Know Sex Of A Pig By Viewing Bamfiles
... unless the animals are 100% inbred. it is possible to determine sex by counting heterozygous X sites. If they are mostly homo -> likely male; if a decent fraction is heterozygous -> likely female; This is how plink determine sex using genotypes. ...
written 4.8 years ago by Wen.Huang1.1k
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Order Of Realignment/Markduplicates/Recalibration
... Hi all, I am wondering what is the best order to do alignment processing. GATK best practice v4 (http://www.broadinstitute.org/gatk/guide/topic?name=methods-and-workflows) have different sequences when doing single-lane or multi-sample processing. I don't think the order of recal and dedup matters. ...
gatk markduplicates written 4.8 years ago by Wen.Huang1.1k • updated 4.8 years ago by Andreas2.3k
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Answer: A: Bwa-0.6.1-Tpx.Patch
... put this file in the Makefile directory run patch bwa-0.6.1-tpx.patch make ...
written 4.9 years ago by Wen.Huang1.1k
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Answer: A: Remove Vcf Header Lines
... how about sed '/^#/d' your.vcf > noheader.vcf ? ...
written 4.9 years ago by Wen.Huang1.1k

Latest awards to Wen.Huang

Supporter 3.7 years ago, voted at least 25 times.
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: Filtering Fastq Sequences Based On Lengths
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Converting Blast Output To Sam Format
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: How To Know Sex Of A Pig By Viewing Bamfiles
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: Conduct Hardy-Weinberg Equilibrium Test On Imputed (Mach) Snp Data?
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering
Appreciated 5.2 years ago, created a post with more than 5 votes. For A: Read Group In Sam/Bam Files: What Do They Exactly Describe?
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: Read Group In Sam/Bam Files: What Do They Exactly Describe?
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: Why Are There Many Rna-Seq Hits To Intronic Regions?
Appreciated 5.2 years ago, created a post with more than 5 votes. For A: How To Interpret Snps
Good Answer 5.2 years ago, created an answer that was upvoted at least 5 times. For A: How To Interpret Snps
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: How To Interpret Snps
Teacher 5.3 years ago, created an answer with at least 3 up-votes. For A: Cufflinks Transcript Assembly
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: How To Define Percent-Identity From A Cigar String/ A Bam/Sam File?
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: Estimate Insert Size In Paired-End/Mate-Pair
Good Answer 5.5 years ago, created an answer that was upvoted at least 5 times. For A: How To Download All The Introns From Ucsc
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: How To Download All The Introns From Ucsc
Appreciated 5.5 years ago, created a post with more than 5 votes. For A: How To Download All The Introns From Ucsc
Student 5.5 years ago, asked a question with at least 3 up-votes. For Database For Causal Genetic Variants
Appreciated 5.7 years ago, created a post with more than 5 votes. For A: Bed Files And Flanking Regions
Teacher 5.7 years ago, created an answer with at least 3 up-votes. For A: Bed Files And Flanking Regions
Good Answer 5.7 years ago, created an answer that was upvoted at least 5 times. For A: Bed Files And Flanking Regions

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