User: Rahul Sharma

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Rahul Sharma560
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Germany and India
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http://www.bik-f.de/ro...
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Last seen:
19 hours ago
Joined:
6 years, 7 months ago
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Posts by Rahul Sharma

<prev • 80 results • page 1 of 8 • next >
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Comment: C: 25 DE genes with 8 samples and 4 DE genes with 16 samples
... Which software are you using for finding DEGs? Maybe it would be helpful to compare different software outputs. How these samples are placed in a PCA plot? I would also look into the read count for individual replicates and see how the read counts are different in each replicate of the 4 DEGs. I use ...
written 1 day ago by Rahul Sharma560
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Job: Bioinformatician job offer at Genome Biologics, Frankfurt, Germany
... **Bioinformatician - Genome Biologics - Redefining Drug Development** Position type: permanent, 100%, based in Frankfurt (DE). Genome Biologics is a Biotherapeutics company headquartered in Germany with a strong background and proven track record in silico drug screening, in vivo preclinical drug t ...
bioinformatic next-gen job rna-seq written 12 weeks ago by Rahul Sharma560
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Ribo-seq couts are more than RNA-seq count
... I am analysing Ribo-Seq data (Illumina single end ~25 bp reads) using the Xtail pipeline. I also have RNA-Seq data sequenced using the same samples and sequencing chemistry (Illumina single end ~25 bp reads). During the bioinformatic analyses, we figured out that in around 48% of genes the Ribo-seq ...
ribo-seq ngs data analysis xtail rna-seq written 5 months ago by Rahul Sharma560 • updated 1 day ago by afeizi0
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Answer: A: Formula to calculate FPKM
... Although I would use DESeq2, Cuffdiff or other published and well established methods for finding DEGs. Here is a link where they explained the formula in details: [RPKM, FPKM and TPM, clearly explained][1] [1]: http://www.rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained/ ...
written 6 months ago by Rahul Sharma560
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Answer: A: gene expression database for quary a gene
... Although that is very tricky to get gene signatures that could match to your query signatures, as many factor influence the expression profiles e.g cell type used, controls, number of replicates and way of generating expression profiles. Here are few on-line resources that I use for my analyses: ht ...
written 6 months ago by Rahul Sharma560
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Answer: A: gene ortholog conversion
... As mentioned by Jean-Karim, orthologs are genes that derive from a common ancestor by speciation. You could see multiple copies (paralogs) derived from gene duplication events. Although ensembl generate a list of all orthologs, however if you are interested in filtering on certain percentage identit ...
written 6 months ago by Rahul Sharma560
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Answer: A: Tophat2 shows error during running
... Here is a quick solution without installing/re-installing different versions of python: # Create a new environment for python 2.7 >conda create -n py2 python=2.7 anaconda #To activate this environment, use: > source activate py2 >conda install -c bioconda tophat ...
written 9 months ago by Rahul Sharma560 • updated 9 months ago by Ram17k
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DeSEq2 unexpressed genes and unchnaged gene expression
... Hi all, I am interested in investigating differentially expressed genes, un-expressed genes and unchanged (same as control) genes among four samples (three replicates each) let's say A, B, C and D. I carried out an DEG analysis by taking A as control and calculated all fold change values w.r.t the ...
gene expression deseq2 rna-seq written 10 months ago by Rahul Sharma560
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Answer: A: Is there any tool to calculate dn/ds for orthologues?
... Few years ago I used the codeml module of PAML tool to carry out selection analyses on several fungal species [Published_work][1]. There are several models (site model, branch-site model, branch model and clade model) that one could select on the basis of your aim of the analysis. You can detect sel ...
written 13 months ago by Rahul Sharma560
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Answer: A: Convert Gff3 (Augustus Output File) To Feature Table File (.Tbl) - Genbank Submi
... That could be done by using the [EMBOSS seqret][1]. Following are few examples: For EMBL format conversion: seqret -sequence test.fasta -feature -fformat gff -fopenfile test.gff -osformat embl -auto For Genbank format conversion: seqret -sequence test.fasta -feature -fformat gff -fopenfi ...
written 15 months ago by Rahul Sharma560

Latest awards to Rahul Sharma

Epic Question 4 months ago, created a question with more than 10,000 views. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Scholar 6 months ago, created an answer that has been accepted. For A: gene ortholog conversion
Popular Question 9 months ago, created a question with more than 1,000 views. For MIRA for metagenome assembly
Popular Question 9 months ago, created a question with more than 1,000 views. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Great Question 12 months ago, created a question with more than 5,000 views. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Appreciated 21 months ago, created a post with more than 5 votes. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Good Question 21 months ago, asked a question that was upvoted at least 5 times. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Popular Question 24 months ago, created a question with more than 1,000 views. For Does Velvet Assembler Use Ram Of All Nodes Altogether?
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Download All The Bacterial Genomes From Ncbi
Great Question 2.2 years ago, created a question with more than 5,000 views. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Download All The Bacterial Genomes From Ncbi
Great Question 2.4 years ago, created a question with more than 5,000 views. For How To Extract Cds And Protein Sequences From Cufflinks Transcripts.Gtf File?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Denovo Assembly Of Paired And Mate Paired Reads
Popular Question 3.3 years ago, created a question with more than 1,000 views. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Student 3.3 years ago, asked a question with at least 3 up-votes. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?

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