User: Rahul Sharma

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Rahul Sharma540
Reputation:
540
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Trusted
Location:
Germany and India
Website:
http://www.bik-f.de/ro...
Scholar ID:
Google Scholar Page
Last seen:
an hour ago
Joined:
6 years, 4 months ago
Email:
r***********@gmail.com

Posts by Rahul Sharma

<prev • 78 results • page 1 of 8 • next >
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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 9 weeks ago by Rahul Sharma540 • updated 9 weeks ago by Carlo Yague4.0k
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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 3 months ago by Rahul Sharma540
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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 3 months ago by Rahul Sharma540
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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 3 months ago by Rahul Sharma540
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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 6 months ago by Rahul Sharma540 • updated 6 months ago by Ram15k
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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 6 months ago by Rahul Sharma540
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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 10 months ago by Rahul Sharma540
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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 11 months ago by Rahul Sharma540
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Answer: A: Calculate numbers of indels <=2 nt within sam
... Few months ago I did some SNP analyses using mapped sam files. I compared two samples say prep2 and prep3, using samtools and bcftools. Following are the commands I used to investigate all variations including INDELS with a coverage cut-off of 100 and mapping quality cutoff 20. You could grep INDEL ...
written 12 months ago by Rahul Sharma540
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Answer: A: extract SNP, variants
... I am also doing SNP analyses, I used following commands which could be of your interest, please adjust the input parameters accordingly: # In the following commands I am comparing two samples, prep2 and prep3, in this example I already have mapped .bam files. In case you have a single sample or fil ...
written 14 months ago by Rahul Sharma540

Latest awards to Rahul Sharma

Epic Question 6 weeks ago, created a question with more than 10,000 views. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Scholar 3 months ago, created an answer that has been accepted. For A: gene ortholog conversion
Popular Question 5 months ago, created a question with more than 1,000 views. For MIRA for metagenome assembly
Popular Question 6 months ago, created a question with more than 1,000 views. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Great Question 9 months ago, created a question with more than 5,000 views. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Appreciated 18 months ago, created a post with more than 5 votes. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Good Question 18 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 20 months ago, created a question with more than 1,000 views. For Does Velvet Assembler Use Ram Of All Nodes Altogether?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Download All The Bacterial Genomes From Ncbi
Great Question 23 months ago, created a question with more than 5,000 views. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Download All The Bacterial Genomes From Ncbi
Great Question 2.1 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 2.6 years ago, created a question with more than 1,000 views. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Denovo Assembly Of Paired And Mate Paired Reads
Popular Question 3.0 years ago, created a question with more than 1,000 views. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Student 3.0 years ago, asked a question with at least 3 up-votes. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Popular Question 3.7 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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