User: BioRyder

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BioRyder160
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Posts by BioRyder

<prev • 51 results • page 1 of 6 • next >
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How to imporve the P threshold value in FarmCPU (GWAS)
... Hello Team, I am running a GWAS analysis on a diploid plant with FarmCPU and I got result with no significant SNPs ( See attached QQ plots of [RED][1] & [GREEN][2] ). I would like to know how can I improve the P threshold value by using FarmCPU ? Details o f my GWAS study is below : The p ...
farmcpu multilocus mlm gwas written 4 months ago by BioRyder160
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Identify K value from ADMIXTURE cross-validation result
... Hello , I ran ADMIXTURE software ( population structure) with cross-validation test and got the following result. From this result which value I should use for K (3 or 4)? [https://wcmq.box.com/s/nw284b0n80a5cji5i3jjb4u3cywzxxno][1] **Pop : Std.error** (K=1) : 0.4946 (K=2) : 0.46638 (K= ...
population structure k value admixture written 5 months ago by BioRyder160 • updated 5 months ago by toralmanvar770
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Structure Software : Error in assigning memory (not enough space?)
... Hello Team, I am getting the below mentioned error while running the structure software [V2.3.4] (used strauto) with NUMINDS : 170, and NUMLOCI : 780897, INFILE : File1 parameter (mainparams) .At the same time I am able to run with same parameter (mainparams) with NUMINDS : 135 and NUMLOCI : 564 ...
structurre population structure software strauto written 5 months ago by BioRyder160
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(Closed) Is any other way to reduce genomic inflation other than PCA in GWAS ?
... Hello , We are doing GWAS (PLINK) in a plant with fruits color phenotype. Is any other way to reduce genomic inflation other than PCA ? ...
gwas genomic inflation plink written 6 months ago by BioRyder160
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How to choose best PCA for reducing genomic inflation
... Hello , We are doing GWAS study related to fruits colour by using PLINK 1.9. Color intensity (RED, GREEN & BLUE channel ) of fruit's color is used as phenotype for this study. The genomic inflation is **2.2** after association test (--pheno pheno.txt --linear hide-covar --adjust qq-plot --all- ...
gwas associtaion study genomic inflation plink pca written 6 months ago by BioRyder160 • updated 6 months ago by Kevin Blighe45k
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Comment: A: Dual index barcode demultiplex issue
... Thank you so much @Devon Ryan.Your answer is more clear and correct.I went through the illumina doc, [which you mentioned][1], and it mentioned as below.Hope fully it will help others in future.Here is the illumina conclusion: Sequencing on the MiniSeq, NextSeq, and HiSeq 3000/4000 systems follow a ...
written 13 months ago by BioRyder160
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Dual index barcode demultiplex issue
... Hello, Following are the list of dual indexed illumina libraries we have used for illumina run.But we were not able demultiplex the data by using the barcodes.Because 99% of the data going as undetermined. Index1 ------ Index2 ( case1 ) ATGAGC ---- TGAACCTT ATTCCT ---- TGAACCTT CAAAA ...
bcltofastq hiseq4000 dual index barcod demultiplex written 13 months ago by BioRyder160
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Answer: A: gtf file for cufflink
... Here you can find : http://genome.ucsc.edu/cgi-bin/hgTables?command=start ...
written 3.2 years ago by BioRyder160
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Comment: C: Bcl to fastq conversion problem in bcl2fastq-2.17
... Hi All, We have identified the problem.The above mentioned problem is happened due to File format of linux Server. Bcl2fast Version is working properly in XFS file system. But If we are using gpfs file system in Linux server,bcl2fastq V2 is generating partial out put file, missing R1 or both R1 and ...
written 3.2 years ago by BioRyder160
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Answer: A: RNA-Seq for DE analysis
... Hello, The below biostars post will help you to know about RNA seq and DE. https://www.biostars.org/p/174376/#174800 ...
written 3.3 years ago by BioRyder160

Latest awards to BioRyder

Popular Question 4 months ago, created a question with more than 1,000 views. For bcl to fastq Conversion
Supporter 5 months ago, voted at least 25 times.
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: trimming the paired end reads with cutadapt
Popular Question 23 months ago, created a question with more than 1,000 views. For bcl2fastq-V2 base mask issue for six and eight barcode length
Popular Question 23 months ago, created a question with more than 1,000 views. For bcl to fastq Conversion
Popular Question 23 months ago, created a question with more than 1,000 views. For Canu Pacbio assembly
Popular Question 23 months ago, created a question with more than 1,000 views. For base mask option in bcl to fastq conversion
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Canu Pacbio assembly
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Canu Pacbio assembly
Popular Question 2.7 years ago, created a question with more than 1,000 views. For bcl2fastq-V2 base mask issue for six and eight barcode length
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Bcl to fastq conversion problem in bcl2fastq-2.17
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: trimming the paired end reads with cutadapt
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: trimming the paired end reads with cutadapt
Autobiographer 3.4 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 3.4 years ago, created an answer that has been accepted. For A: bcl2fastq-V2 How to skip some line
Scholar 3.5 years ago, created an answer that has been accepted. For A: bcl2fastq-V2 How to skip some line

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