User: Karma

gravatar for Karma
Karma270
Reputation:
270
Status:
Trusted
Location:
India
Last seen:
1 month ago
Joined:
2 years, 7 months ago
Email:
s******@gmail.com

Posts by Karma

<prev • 52 results • page 1 of 6 • next >
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Comment: C: How to rename multiple fastq files
... Oh sorry. I did not see your comment. ...
written 5 weeks ago by Karma270
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Comment: A: Where to download Normal exome bam for creating PoN (Panel of Normals) for cance
... I suggest you to use data from http://www.internationalgenome.org/data-portal/sample or from https://www.ebi.ac.uk/ega/datasets ...
written 6 weeks ago by Karma270 • updated 6 weeks ago by RamRS26k
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Comment: C: How to pass arguments in a bash script to perform read alignment to the referenc
... I managed to run this by running sudo chmod 777 exome_pipeline.sh and executed the scrpit `sh exome_pipeline.sh` ...
written 6 weeks ago by Karma270
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Comment: A: What Agilent Interval Files (.Bed) Should I Use For Exome Variant Calling With G
... You can use `regions` mentioned in the website ...
written 6 weeks ago by Karma270
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Comment: C: How to pass arguments in a bash script to perform read alignment to the referenc
... Is it not possible to create pipeline with plain bash scripting? ...
written 6 weeks ago by Karma270
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Comment: C: How to pass arguments in a bash script to perform read alignment to the referenc
... I cross checked `outputDir` is available as directory. I just manually created a directory '`AB132`' inside `outputDir` and executed the script again. I don't know it is working!!!. The directories are `not in the root folder` if it is related to any permission issues. ...
written 6 weeks ago by Karma270
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How to pass arguments in a bash script to perform read alignment to the reference?
... My plan to is to make automated pipeline for processing exome data to derive the vcf file. I coded the alignment step in the following way #!usr/bin/bash reference="/media/ngs/ref/Homo_sapiens_assembly19/Homo_sapiens_assembly19.fasta" outputDir=$1 sampleID=$2 ...
exome data analysis bwa bash written 6 weeks ago by Karma270
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What is the possibility of replicates being different from other replicates of same sample?
... I have analyzed the dataset of **GSE38132** from gene expression omnibus. The is from **cell line breast cancer ZR-75-1** which comprises of **9 conditions** with **4 replicates** for each condition making it **36 samples**. I used limma package to normalize the data (**quantile normalization**). I ...
replicates microarray mean error written 6 weeks ago by Karma270
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How to perform normalization and calculate when there are multiple groups ?
... I have 4 sample [*control, pre-treatment, post-treatment, metastais*] with 4 replicates which make total 4x4 = 16 samples I want to perform comparison of control with all other groups. For the said purpose should I perform normalization of all samples and perform **ANOVA** to find significant DEGs i ...
anova rna-seq normalization written 7 weeks ago by Karma270
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Answer: A: Building Dict File for GATK
... Change your command to the following: java -jar picard.jar CreateSequenceDictionary R=Homo_sapiens_assembly18.fasta O=Homo_sapiens_assembly18.dict ...
written 11 weeks ago by Karma270

Latest awards to Karma

Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Building Dict File for GATK
Popular Question 19 months ago, created a question with more than 1,000 views. For How to use GRCh38 as reference for Annotating the variants using Annovar?
Popular Question 19 months ago, created a question with more than 1,000 views. For Where can I download Clinical or Medical Exome?
Popular Question 19 months ago, created a question with more than 1,000 views. For RNA-Seq or Exome Seq for Clinical data analysis
Popular Question 19 months ago, created a question with more than 1,000 views. For RNA-Seq or Exome Seq for Clinical data analysis
Popular Question 20 months ago, created a question with more than 1,000 views. For RNA-Seq or Exome Seq for Clinical data analysis
Student 2.6 years ago, asked a question with at least 3 up-votes. For RNA-Seq or Exome Seq for Clinical data analysis

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