User: Rahul Sharma

gravatar for Rahul Sharma
Rahul Sharma520
Reputation:
520
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Trusted
Location:
Germany and India
Website:
http://www.bik-f.de/ro...
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Google Scholar Page
Last seen:
1 day, 2 hours ago
Joined:
5 years, 11 months ago
Email:
r***********@gmail.com

Posts by Rahul Sharma

<prev • 74 results • page 1 of 8 • next >
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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 4 weeks ago by Rahul Sharma520 • updated 4 weeks ago by Ram13k
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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 7 weeks ago by Rahul Sharma520
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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 5 months ago by Rahul Sharma520
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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 6 months ago by Rahul Sharma520
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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 7 months ago by Rahul Sharma520
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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 9 months ago by Rahul Sharma520
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Comment: C: MSA processing algorithms in perl
... Many thanks for your kind reply! I did that with perl arrays. Regards, Rahul ...
written 13 months ago by Rahul Sharma520
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MSA processing algorithms in perl
... Dear all, I have been working on several MSA files (3000 orthologs Msa files in phylip format of 7 genomes) in which I have to get a highly conserved sequence on the basis of certain parameters. I want to write a perl script to fulfill all my needs, I know Gblocks (http://molevol.cmima.csic.es/cast ...
perl msa algorithms written 13 months ago by Rahul Sharma520
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MIRA for metagenome assembly
... Hi all, I am working on a de novo metagenome assembly project. In this data I am expecting several species of bacteria. The sequencing data I have received have been sequenced with Illumina 100-300 bp inserts with a read length of around 150 bps. I was giving a try to MIRA genome assembler, however ...
next-gen metagenome mira written 2.3 years ago by Rahul Sharma520
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Comment: C: Get Query Coverage From Local Blast
... Hi Raju, Please add column headers, I am wondering if you had used the default parameters or specified your own set of columns. Wishes, Rahul ...
written 3.6 years ago by Rahul Sharma520

Latest awards to Rahul Sharma

Popular Question 25 days ago, created a question with more than 1,000 views. For MIRA for metagenome assembly
Popular Question 6 weeks ago, created a question with more than 1,000 views. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Great Question 4 months ago, created a question with more than 5,000 views. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Appreciated 13 months ago, created a post with more than 5 votes. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Good Question 13 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 15 months ago, created a question with more than 1,000 views. For Does Velvet Assembler Use Ram Of All Nodes Altogether?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Download All The Bacterial Genomes From Ncbi
Great Question 18 months ago, created a question with more than 5,000 views. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Download All The Bacterial Genomes From Ncbi
Great Question 20 months 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 2.2 years ago, created a question with more than 1,000 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: Denovo Assembly Of Paired And Mate Paired Reads
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?
Student 2.6 years ago, asked a question with at least 3 up-votes. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Merge Velvet Assemblies
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Merge Velvet Assemblies

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