User: Saad Khan

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Saad Khan400
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Posts by Saad Khan

<prev • 131 results • page 1 of 14 • next >
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Is it possible to introduce mutations (SNV/Indels) in precomputed lastz alignments
... Hi, I have multiple resequencing files from multiple species that I am trying to compare. For each individual vcf file I generate a alternate fasta using FastaAlternateReferenceMaker. I was wondering if there is a tool/package that can introduce the mutations (indel/snv) in the precomputed alignmen ...
fastaalternatereferencemaker lastz pairwise_align written 11 months ago by Saad Khan400
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Comment: C: Merging variant calls of whole exome and RNA-seq
... @archie This probably does not do what I want. I only need to merge the RNA and exome vcf file so that I can make a consensus fasta file from it using FastaAlternateReferenceMaker in GATK. ...
written 16 months ago by Saad Khan400
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Merging variant calls of whole exome and RNA-seq
... Hi, I have many samples for which I have whole-exome and corresponding RNA-seq data I have already done GATK variant calling using their best practices and recommendations. Now I would like to merge the variants from the two approaches. I know the merging may not be straightforward because of RNA-s ...
snvs gatk variants rna-seq indels written 17 months ago by Saad Khan400 • updated 17 months ago by archie90
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Comment: C: Negative dataset selection
... Hi @Jean-Karim Heriche I have edited the question to provide more information. Looking forward to your reply. Thanks! ...
written 18 months ago by Saad Khan400
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Negative dataset selection
... Hi, I am working on a classification problem using a sequence data. I have the positive data which belongs to a gene region I also have negative data which I have selected based upon the most common 5 nucleotides in the center. It seems like my model is over fitting and giving me very high accuracy ...
machine-learning sequence classification rna dna written 18 months ago by Saad Khan400
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Which tool to use to get all citations of a pmid paper?
... Hi, I have thousands of pmid which are associated with a disease. For each pmid I need to find how many times it has been cited in a publication in order to assign importance to that particular pmid. I was wondering what available methods/tools are there that can give me this information. I have tr ...
entrez eutils efetch written 22 months ago by Saad Khan400 • updated 22 months ago by h.mon30k
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Tool for generating Physicochemical properties from sequence of RNA/DNA
... Hi, I am trying to generate some machine learning features for my prediction problem. I was planning to use physicochemical properties of the sequence of nucleotide for doing that. I was wondering what tools are available that could help me do that. Thanks! ...
mrna physicochemical properties sequence dna written 2.3 years ago by Saad Khan400
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Comment: C: Most genes with entrez id in KEGG database don't have a pathway assigned. Is the
... We did contrast mining between cases and controls for a neurological disorder in which we found SNP associations between a list of gene pairs. We want to do module enrichment for those gene pairs. Many of the genes identified in these gene pairs do not have a reactome_id or kegg pathway id associate ...
written 2.4 years ago by Saad Khan400
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Most genes with entrez id in KEGG database don't have a pathway assigned. Is there a tool already available that uses textmining to assign pathway to genes.
... Hi, I was working with bioconductor package KEGGREST in trying to find gene 2 pathway mappings. In Kegg according to KEGGREST there are only 7364 genes which are present in the 317 pathways. There are a total of 39556 genes in KEGG I was wondering how can I find pathways for the rest of the genes ...
keggrest reactome kegg written 2.4 years ago by Saad Khan400
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Comment: C: Protein protein interaction conservation scores
... I am more interested in looking at protein interaction conservation. Which I believe would be similar for species like human and mice for which interactome data is well defined.There has been some research in the area where people have used/calculated PPI similarity measure but these were done using ...
written 3.4 years ago by Saad Khan400

Latest awards to Saad Khan

Popular Question 7 months ago, created a question with more than 1,000 views. For chain files for mouse mm9 to ensembl version 75
Popular Question 7 months ago, created a question with more than 1,000 views. For chain files for mouse mm9 to ensembl version 75
Popular Question 11 months ago, created a question with more than 1,000 views. For chain files for mouse mm9 to ensembl version 75
Popular Question 15 months ago, created a question with more than 1,000 views. For liftover chain files for mouse mm9 to ensembl version 75
Popular Question 15 months ago, created a question with more than 1,000 views. For chain files for mouse mm9 to ensembl version 75
Popular Question 15 months ago, created a question with more than 1,000 views. For Contact residue map of mutated protein around active sites
Popular Question 16 months ago, created a question with more than 1,000 views. For chain files for mouse mm9 to ensembl version 75
Popular Question 16 months ago, created a question with more than 1,000 views. For chain files for mouse mm9 to ensembl version 75
Popular Question 17 months ago, created a question with more than 1,000 views. For Transcriptional repressors and transcriptional activators
Popular Question 17 months ago, created a question with more than 1,000 views. For liftover chain files for mouse mm9 to ensembl version 75
Popular Question 17 months ago, created a question with more than 1,000 views. For How does vcf-stats give snp count
Popular Question 17 months ago, created a question with more than 1,000 views. For chain files for mouse mm9 to ensembl version 75
Great Question 21 months ago, created a question with more than 5,000 views. For small RNA-seq pipelines
Popular Question 21 months ago, created a question with more than 1,000 views. For Transcriptional repressors and transcriptional activators
Popular Question 21 months ago, created a question with more than 1,000 views. For liftover chain files for mouse mm9 to ensembl version 75
Popular Question 21 months ago, created a question with more than 1,000 views. For liftover chain files for mouse mm9 to ensembl version 75
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Visualizing microRNA expression network
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How does vcf-stats give snp count
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Transcriptional repressors and transcriptional activators
Popular Question 2.3 years ago, created a question with more than 1,000 views. For liftover chain files for mouse mm9 to ensembl version 75
Great Question 2.3 years ago, created a question with more than 5,000 views. For small RNA-seq pipelines

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