User: deepkumar1983

gravatar for deepkumar1983
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New User
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United States
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10 months, 1 week ago
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3 years, 8 months ago
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Posts by deepkumar1983

<prev • 13 results • page 1 of 2 • next >
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Comment: C: GATK SNPs calling multiple sample without any known SNPs database
... Thanks for the help. I wish to know that whether the recalibration should be done on each sample separately or all the three could be combine in a single command. In first case, I got three read group table while in the 2nd it give one read group table. In your opinion which is good. ...
written 10 months ago by deepkumar198340
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GATK SNPs calling multiple sample without any known SNPs database
... I am working on identifying the SNPs in the genome of an insect which is sequenced in three samples. Following the GATK best practice pipeline i have completed the following task. 1. Quality filtered reads. 2. Read Alignment for each sample eg. S1, S2, S3. 3. Sort and mark duplicates in each sam ...
gatk multiple-sample bsqr snp written 10 months ago by deepkumar198340 • updated 10 months ago by YaGalbi1.4k
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Signal Sequence in sORF-encoded peptides or micropeptides
... Hi I am exploring the sORF-encoded peptides which are less than 100 AAs long. As i read these kind of peptides are the direct product of gene; they did not came from processing of large precursor proteins. So, i need to clarify my doubt whether the signal peptides are present in this type of peptid ...
gene genome sequence rna-seq written 21 months ago by deepkumar198340
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CNVnator_Error in histogram
... Hi I am using the CNVnator tool for copy number variation. My Coomand is these 1. cnvnator -root out.root -genome GCA_000003055.5_Bos_taurus_UMD_3.1.1_genomic.fna -chrom GK000001.2 -unique -tree mem_snp_against_ref.bam 2. cnvnator -root out.root -genome GCA_000003055.5_Bos_taurus_UMD_3.1.1_genomi ...
software error written 3.0 years ago by deepkumar198340 • updated 3.0 years ago by Mike1.3k
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Error in Calculation of Ka/Ks value using Ka/Ks calculator
... Hi, I am using Ka/Ks calculator software for identification of rapidly evolving genes. I align my gene sequences with muscle software and then after converting to axt format used this tool. I am surprised that it work well with some alignment and for others this give me an error "**Error. The s ...
software error written 3.1 years ago by deepkumar198340 • updated 7 months ago by ashatan.3140
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input tree for CAFE phylogenetic analysis
... Hi  I am working on identification of gene expansion and contraction family using CAFE. As this software need the input tree with branch-length. I have use single gene family and built the tree for each family using phylip proml and finally a consensus tree made using consensus program of phylip. T ...
alignment myposts written 3.2 years ago by deepkumar198340 • updated 10 weeks ago by Biostar ♦♦ 20
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Evolutionary Phylogenetic tree
... Hi friends I want to build a evolutionary phylogenetic tree. for this i am following this article "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514880/". According to this, I have selected single gene orthologus family and use muscle for each family alignment and build tree with Phylip JTT model. ...
genome alignment sequence written 3.2 years ago by deepkumar198340 • updated 3.2 years ago by moranr250
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Comment: C: ChickPea DEG Analysis
... Thanks for the reply. But i have no replicates.   ...
written 3.6 years ago by deepkumar198340
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ChickPea DEG Analysis
... Hi, I have chickpea  rnaseq data of control vs treated without any replicate. I had used HTseqCount for count the gene and want to use edgeR for identifying DEG. My question is what should be the ideal value for dispersion parameter because it was mentioned in edgeR manual that for  well-controlled ...
edger written 3.6 years ago by deepkumar198340 • updated 3.6 years ago by PoGibas4.8k
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Comment: C: Quality contraol on 454 data
... Hi this is the link of the file https://www.dropbox.com/s/h6q97psk3gadf3h/Outputfile_fastqc.html?dl=0 My Pipeline Commands are java -jar /opt/software/Trimmomatic-0.32/trimmomatic-0.32.jar SE SRR1646514.fastq SRR1646514_filter1.fastq ILLUMINACLIP:/opt/software/Trimmomatic-0.32/adapters/TruSeq2-SE ...
written 3.7 years ago by deepkumar198340

Latest awards to deepkumar1983

Popular Question 21 months ago, created a question with more than 1,000 views. For Error in Calculation of Ka/Ks value using Ka/Ks calculator
Popular Question 21 months ago, created a question with more than 1,000 views. For Quality control on 454 data

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