User: Manvendra Singh

gravatar for Manvendra Singh
Manvendra Singh2.1k
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Location:
Berlin, Germany
Twitter:
manvendr7
Last seen:
9 months ago
Joined:
6 years, 9 months ago
Email:
m*****@gmail.com

PhD Student (Mobile DNA Group) at Max-Delbruck Centre fur Molecular Medicine

Posts by Manvendra Singh

<prev • 386 results • page 2 of 39 • next >
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Answer: A: Ensembl transcript ID - BioMart retrieval
... Hi Dear, I would recommend not to filter anything. Dataset: homo sapiens genes Attributes: Ensembl gene ID. Ensembl transcript ID. first get the data in tsv, and then just remove the duplicates hth ...
written 3.6 years ago by Manvendra Singh2.1k
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Answer: A: Gene expression in populations
... [these literatures should help you [Brain transcriptome][1] [The populations sampled span the geographic breadth of human migration history; EBV transformed lymphoblastoid cell lines derived from 45 individuals in the Human Genome Diversity Panel (HGDP)][2] [1]: http://www.pnas.org/content/112/2 ...
written 3.6 years ago by Manvendra Singh2.1k
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Comment: C: Is there any software/online tools to find N terminal and C terminal of a protei
... Dude, you are confused. May be first you get your question right. Protein is made by reading mRNA in the 5' to 3' direction and making new protein from its amino end (N-terminus) towards its carboxyl end (C-terminus). so In your case, 1st amino acid would have N terminal and 149th would have C-term ...
written 3.6 years ago by Manvendra Singh2.1k
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Answer: A: Differential isoform expression analyses
... Differential Isoform expression is consequence of Alternate splicing If the overall expression of gene is not changing but isoform expression is differential then its the case isoform switch in your case. you can perform gene set enrichment analysis to see if alternatively spliced transcripts are p ...
written 3.7 years ago by Manvendra Singh2.1k
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Answer: A: Identify the isoform of a transcript using RNA Seq data
... Did you try running Cufflinks2 RABT assembly; I would suggest you to run in both mode; default and RABT and see if you can catch your desired isoform ...
written 3.8 years ago by Manvendra Singh2.1k
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Comment: C: Comparing gene expression profiles between species
... Its just mean of all transcripts to assign one value to gene PS: Its quite old post, now this job is done by featureCount where we calculate counts on gene_id but not on transcript_id given in gtf files ...
written 3.8 years ago by Manvendra Singh2.1k
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Answer: A: Merging expression data from multiple platforms
... May be assign, mean of all probes to its target gene. then choose only those genes that are detectable in all platforms. once you have equal number of rows in different datasets, you can easily merge it by "merge" function in R ...
written 3.8 years ago by Manvendra Singh2.1k
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Answer: A: Time series microarray data
... Canser ? If you mean Cancer progression timed series data, you can look into TCGA datasets Tier4 has normalized expression data https://tcga-data.nci.nih.gov/docs/publications/tcga/? ...
written 3.8 years ago by Manvendra Singh2.1k
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Comment: C: GO analysis- analyze upregulated and downregulated genes separately?
... Yes, I have seen some papers where upregulated and downregulated genes are categorized separately on GO term; Once you get significant level of GO term in the subset of genes, you can go for pathway or network analysis to see the enrichment of your detected genes in certain pathway or process ...
written 4.8 years ago by Manvendra Singh2.1k
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Why the resuming tophat2 command gives a strange error of samtools version?
... Hi All, I was mapping paired end fastq files by tophat2 on 10 threads, it got stucked during Searching for junctions via segment mapping. Everything seems to be alright; Here is the output [2015-08-19 00:16:41] Beginning TopHat run (v2.0.8) ----------------------------------------------- [2015-08- ...
tophat2 resume mapping rna-seq written 4.8 years ago by Manvendra Singh2.1k

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Good Answer 23 months ago, created an answer that was upvoted at least 5 times. For A: convert FASTA into FASTQ using linux
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: What should I looking for at the beginning (Master degree in Computer Science)
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Scholar 3.0 years ago, created an answer that has been accepted. For A: Where to download In-vitro RNA-seq published experiments?
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Popular Question 3.5 years ago, created a question with more than 1,000 views. For How To Get ~ 100% Conserved Genomic Regions Between Human (Hg19) And Mouse(Mm10)?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Why the resuming tophat2 command gives a strange error of samtools version?
Good Answer 3.8 years ago, created an answer that was upvoted at least 5 times. For A: cuffcompare output results
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