User: always_learning

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Posts by always_learning

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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... rna_vm <- vm(rna) Show Traceback Rerun with Debug Error in voom(x, d, plot = F) : Need at least two genes to fit a mean-variance trend I am getting above error while running vm function. Can some one help me on this ? ...
written 4 weeks ago by always_learning790
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Comment: C: Extract KEGG Enzyme data
... import sys f=open(sys.argv[1]) arr=[] for i in f: j = i.strip("\n").split('\t')[1] arr.append(j) print [arr[i:i + 3] for i in xrange(0, len(arr), 3)] This should work for you, assuming that you files is tab seperated file. ...
written 3 months ago by always_learning790
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Comment: C: Error in DADA2
... Can you try this please ? out <- filterAndTrim(fnFs, filtFs, fnRs, filtRs, truncLen=c(240,160), maxN=0, maxEE=c(2,2), truncQ=2, rm.phix=TRUE, compress=TRUE, multithread=FALSE)" ...
written 3 months ago by always_learning790
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Answer: A: Error in DADA2
... mc.cores > 1 is not available for windows. You may try as mc.cores = 1 something like below may work. mcmapply(fastqPairedFilter, mapply(c, fwd, rev, SIMPLIFY = FALSE), mc.cores = 1 ) Can you please try above and let us know. ...
written 3 months ago by always_learning790 • updated 3 months ago by genomax33k
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Answer: A: ROH ( Runs of Homozygosity Analysis)
... Hi I know about all these tools. I am moreover asking about how you will interpret results from these tools ? Is their any tutorials somewhere which can help me to understanding this ? Thanks ...
written 3 months ago by always_learning790
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ROH ( Runs of Homozygosity Analysis)
... Dear All, I want to know about ROH analysis ? How to perform it ? How to interpret out put ROH resut data from tools like plink and bcftols roh etc etc. Is their any tutorial or papers available to learn understand and learn these concepts ? Thanks Najeeb ...
wgs roh written 4 months ago by always_learning790
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Comment: C: GATK - gene panel VCF - too many variants - how to filter out
... You should use bed flle from SureSelect kit. java -jar GenomeAnalysisTK.jar -T HaplotypeCaller \ -R '/home/dee/bioinformatics/_reffiles/hg19/ucsc.hg19.fasta' \ -I '/1234/1234_remdup_recal.bam' \ -o '/1234/1234_remdup_recal.g.vcf' \ --emitRefConfidence GVCF \ --variant_index_ ...
written 4 months ago by always_learning790
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Comment: C: Tool Recommendations For Human Genome Assembly
... As far as I know GATK doesn't do Genome Assembly. ...
written 4 months ago by always_learning790
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Answer: A: Biomart error while convertint transcript ID.
... Thanks, Every one. I got the answer for this one actually my transcript was like values<- c("NM_000350.2","NM_000016.5","NM_004924.4","NM_001106.3","NM_000022.2") and it was not maching with any of records so i just converted this into values = c("NM_000350","NM_000016","NM_004924","NM_00110 ...
written 4 months ago by always_learning790
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Biomart error while convertint transcript ID.
... library("biomaRt") ensembl<- useMart("ensembl", dataset="hsapiens_gene_ensembl") value =read.csv("Refseq.txt", strip.white=TRUE) colnames(value) = c("name") values <- as.vector(value$name) getBM(attributes=c("refseq ...
biomart written 4 months ago by always_learning790

Latest awards to always_learning

Popular Question 26 days ago, created a question with more than 1,000 views. For Gvcf Format From Illumina
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Gvcf Format From Illumina
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Need Help Understanding A Programming Statment Written In R
Scholar 4 months ago, created an answer that has been accepted. For A: Biomart error while convertint transcript ID.
Popular Question 5 months ago, created a question with more than 1,000 views. For Gvcf Format From Illumina
Great Question 6 months ago, created a question with more than 5,000 views. For Installing Bwa On 32 Bit Unix Machine
Good Question 6 months ago, asked a question that was upvoted at least 5 times. For Homozygous Indel/Snp & Heterozygous Indel/Snp
Popular Question 6 months ago, created a question with more than 1,000 views. For Gvcf Format From Illumina
Appreciated 6 months ago, created a post with more than 5 votes. For New Bioinformatics Courses At Cousera
Popular Question 8 months ago, created a question with more than 1,000 views. For Difference Between Target Re-Sequencing And Exome Sequencing !!
Popular Question 9 months ago, created a question with more than 1,000 views. For Using parallel with Mem
Popular Question 11 months ago, created a question with more than 1,000 views. For How To Convert Enzyme Id Of Kegg To Ncbi Protein Id'S
Student 11 months ago, asked a question with at least 3 up-votes. For Gwas Stepwise Tutorial
Great Question 12 months ago, created a question with more than 5,000 views. For Gwas Stepwise Tutorial
Popular Question 12 months ago, created a question with more than 1,000 views. For Gvcf Format From Illumina
Epic Question 12 months ago, created a question with more than 10,000 views. For Homozygous Indel/Snp & Heterozygous Indel/Snp
Popular Question 12 months ago, created a question with more than 1,000 views. For Gvcf Format From Illumina
Appreciated 13 months ago, created a post with more than 5 votes. For New Bioinformatics Courses At Cousera
Popular Question 15 months ago, created a question with more than 1,000 views. For problem while Installing BCFtools/htslib
Popular Question 16 months ago, created a question with more than 1,000 views. For problem while Installing BCFtools/htslib
Popular Question 16 months ago, created a question with more than 1,000 views. For problem while Installing BCFtools/htslib
Great Question 16 months ago, created a question with more than 5,000 views. For Homozygous Indel/Snp & Heterozygous Indel/Snp
Popular Question 17 months ago, created a question with more than 1,000 views. For problem while Installing BCFtools/htslib
Popular Question 17 months ago, created a question with more than 1,000 views. For problem while Installing BCFtools/htslib
Popular Question 19 months ago, created a question with more than 1,000 views. For problem while Installing BCFtools/htslib

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