User: Manvendra Singh

gravatar for Manvendra Singh
Manvendra Singh2.0k
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Location:
Berlin, Germany
Twitter:
manvendr7
Last seen:
3 months, 4 weeks ago
Joined:
5 years, 2 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 1 of 39 • next >
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Comment: C: Gene lists and calculated Ka/Ks ratio per gene
... did you visit this site? It might help, it has nice R scripts https://github.com/a1ultima/kaks_error_bars ...
written 16 months ago by Manvendra Singh2.0k
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Answer: A: retrieve genomic coordinate on mRNA
... It should be very simple 1. download the gtf file and install bedtools 2. convert it to bed using gtf2bed 3. grep -wi 'exon' bed_file_converted_from_gtf > exons.bed 4. intersectBed -a your_iCLIP_coordinates -b exons.bed > your_protein_binding_transcripts.bed hth ...
written 16 months ago by Manvendra Singh2.0k
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Comment: C: Any tools to detect lncRNAs from RNA-seq data?
... If you already have annotations for lncRNA then just calculate its expression by using [RSEM][1] If not then you'd have to run Cufflinks as RABT assembly [1]: http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html ...
written 20 months ago by Manvendra Singh2.0k
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Answer: A: Intersecting vcf files with bedtools
... First may be you get rid of headers As per I remember, I always used one vcf and one bed file to intersect by bedtools May be you use vcftools to intersect two vcf files It has nice command as "vcf-isec" Creates intersections and complements of two or more VCF files Nice documentation is [here][ ...
written 20 months ago by Manvendra Singh2.0k
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Answer: A: Statistical significance in phylogenies
... you can try Bootstrapping, you can choose number of bootstraps, with this you can observe how many resampling would give the similar tree you are expecting. consequently , you can calculate p-values too there is nice package in R that does the needful its called pvclust [its here][1] [1]: htt ...
written 20 months ago by Manvendra Singh2.0k
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Answer: A: STAR aligner fails to produce unmapped file
... try not to use SortedByCoordinate, get the output in sam format try using this argument in your command and lets see if you get --outReadsUnmapped Fastx ...
written 23 months ago by Manvendra Singh2.0k
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Answer: A: getfasta command requires a bedfile template of some sort
... you would have to make your file in "bed" format with atleast 3 coloumns without header viz. # Chr start end add second coloumn as number "1" then bed file would be mm9.bed then you use this comand bedtools getfasta -fi /home/cc16956/mm9.fa -bed /storage/projects/teif/mm9_generic_data/mm ...
written 23 months ago by Manvendra Singh2.0k • updated 23 months ago by genomax57k
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Answer: A: Metabolic gene database: The most-frequently mutated metabolic genes in human ca
... I don't think any such database is there to my knowledge. Mutations could cause cancer (BRCA, BRAF, TP53 etc), cancer could cause mutations (L1 retrotransposition, edited retrogenes etc etc.) your query could be done by downloading somatic mutation database in human cancers from [cosmic][1] then ...
written 2.0 years ago by Manvendra Singh2.0k
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Answer: A: Non-coding RNA Atlas
... is it Genomic sequences and coordinates of lncRNA in human genome? or Expression pattern of each lncRNA in different body organs? anyways you'd get both from UCSC data repository use ucsc table browser under gene prediction track to download lncRNA gtf file and under expression GTEx track to downl ...
written 2.0 years ago by Manvendra Singh2.0k
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Comment: C: Overrepresented sequence in RNA-seq only in R2
... May be first you map your reads against rRNA and tRNA sequences (preferably via bowtie), and discard the mapable reads. If remaining reads still show over-represented sequences then there is something weird, it could also be the case of chimeric transcripts. ...
written 2.0 years ago by Manvendra Singh2.0k

Latest awards to Manvendra Singh

Popular Question 10 months ago, created a question with more than 1,000 views. For Why the resuming tophat2 command gives a strange error of samtools version?
Teacher 16 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)
Scholar 16 months ago, created an answer that has been accepted. For A: Where to download In-vitro RNA-seq published experiments?
Teacher 18 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)
Popular Question 23 months 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 2.1 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 2.1 years ago, created an answer that was upvoted at least 5 times. For A: cuffcompare output results
Teacher 2.5 years 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)
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Limma calls all genes as differentially expressed - what am I doing wrong?
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Scholar 3.7 years ago, created an answer that has been accepted. For A: Where to download In-vitro RNA-seq published experiments?
Scholar 3.7 years ago, created an answer that has been accepted. For A: Where to download In-vitro RNA-seq published experiments?
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Teacher 3.7 years 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)
Scholar 3.8 years ago, created an answer that has been accepted. For A: Where to download In-vitro RNA-seq published experiments?
Popular Question 3.9 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)?
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