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User: banerjeeshayantan

gravatar for banerjeeshayantan
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Posts by banerjeeshayantan

<prev • 219 results • page 1 of 22 • next >
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Comment: C: Mutation calling for pediatric cancer data
... This is an extension of the question that I asked previously. So I have discovered that from the same database that has tumor-germline bam files, I can get tumor-normal vcfs too. So I have tumor1.vcf and germline1.vcf. Similarly, tumor2.vcf and germline2.vcf. This means that each bam file has been a ...
written 29 days ago by banerjeeshayantan • 140
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Comment: C: Mutation calling for pediatric cancer data
... Thanks for your help! ...
written 4 weeks ago by banerjeeshayantan • 140
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Comment: C: Mutation calling for pediatric cancer data
... Got it. So then it's just a different terminology then. Thanks for clarifying that. Now I can just use the GATK pipeline to call somatic variants, right? I guess I was confusing between germline variants and germline samples. ...
written 4 weeks ago by banerjeeshayantan • 140
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Mutation calling for pediatric cancer data
... I have recently gained access to the St Jude children's hospital database with more than 700 paired tumour/germline samples for common and rare pediatric cancers, Up to now, I have called only somatic variants from tumour-normal matched samples using the GATK pipeline. Being new to the field, I am c ...
assembly snp written 4 weeks ago by banerjeeshayantan • 140
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Machine learning using microarray data
... I have developed a classification model using microarray data using a GEO dataset. Let's call this the train set. The class labels were "extreme" vs "not-so-extreme" disease course. Now my advisor has asked me to see the generalizability of the model. But there is no other dataset with the same set ...
machinelearning rna-seq written 4 weeks ago by banerjeeshayantan • 140 • updated 4 weeks ago by Charles Warden ♦ 7.5k
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Machine learning using microarray data
... I am developing machine learning models to classify disease/non-disease patients using gene expression data. I have applied LASSO to select features and built classifiers using some of the top features after feature selection. Now I have to do external validation on an independent test set to judge ...
R rna-seq written 8 weeks ago by banerjeeshayantan • 140 • updated 8 weeks ago by dsull • 630
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Default strand of mutations
... I have downloaded 10000 SNVs from the COSMIC database. These are all cancer-causing variants. Each of these mutations has strand information attached to them. The problem is every mutation has been flagged as belonging to the plus strand. Why is that? Is it a convention? To give you an example, cons ...
genome written 9 weeks ago by banerjeeshayantan • 140
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Distribution of mutations in different parts of the genome
... I have obtained exome sequencing data from 10 normal-tumor samples from patients suffering from pancreatic cancer (PDAC). I am interested in finding the distribution of mutations (single base substitutions specifically) in different parts of the genome (both coding and non-coding). Is there a comput ...
genome written 12 weeks ago by banerjeeshayantan • 140 • updated 12 weeks ago by venu ♦ 6.3k
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Strand information for reference genome
... What is the default strand of the reference genome hg38/hg19? If I am extracting bases from the genome using bedtools getfasta and not specify the strand explicitly, from which strand are the bases getting extracted? ...
assembly sequencing written 3 months ago by banerjeeshayantan • 140 • updated 3 months ago by WouterDeCoster ♦ 42k
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Confusion with fold change cutoff
... I am performing microarray data analysis and I have a set of DEGs using a adjusted pvalue < 0.05. I am getting a total of 152 DEGs. Now I am using different threshold for the log fold change cutoffs. If I am using a log FC of 1, I am getting only 18 DEGs. But if I am including all DEGs (without a ...
R rna-seq written 3 months ago by banerjeeshayantan • 140 • updated 3 months ago by ATpoint ♦ 26k

Latest awards to banerjeeshayantan

Popular Question 23 days ago, created a question with more than 1,000 views. For Checking bam quality
Popular Question 23 days ago, created a question with more than 1,000 views. For Error while downloading data from database[EGA]
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Popular Question 9 weeks ago, created a question with more than 1,000 views. For Update samtools to the latest version
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Popular Question 8 months ago, created a question with more than 1,000 views. For Error while downloading data from database[EGA]
Popular Question 8 months ago, created a question with more than 1,000 views. For Update samtools to the latest version
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