User contributions for Gabre

17 December 2024

• 15:0415:04, 17 December 2024 diff hist −4,864‎ Unix pipes ‎No edit summary current

16 December 2024

• 22:5822:58, 16 December 2024 diff hist +10‎ Unix pipes ‎No edit summary
• 22:5622:56, 16 December 2024 diff hist +136‎ Unix pipes ‎ →‎RSA Checker
• 22:5122:51, 16 December 2024 diff hist −21‎ Unix pipes ‎ →‎RSA Checker
• 22:4922:49, 16 December 2024 diff hist +58‎ Unix pipes ‎ →‎RSA Checker
• 22:4222:42, 16 December 2024 diff hist −369‎ Unix pipes ‎ →‎RSA Checker
• 22:3822:38, 16 December 2024 diff hist +18‎ Unix pipes ‎ →‎Prime Checker (Naive)
• 22:3622:36, 16 December 2024 diff hist +195‎ Unix pipes ‎ →‎RSA Checker
• 16:4216:42, 16 December 2024 diff hist +9‎ Unix pipes ‎ →‎Prime Checker (Naive)
• 16:4116:41, 16 December 2024 diff hist −168‎ Unix pipes ‎ →‎Prime Checker (Naive)
• 16:4016:40, 16 December 2024 diff hist −42‎ Unix pipes ‎ →‎Random Integer Generator
• 16:3816:38, 16 December 2024 diff hist −3,691‎ Unix pipes ‎No edit summary
• 16:2316:23, 16 December 2024 diff hist +191‎ Unix pipes ‎ →‎Real World Example
• 16:1716:17, 16 December 2024 diff hist +29‎ Unix pipes ‎ →‎stderr (Standard Error)
• 16:1316:13, 16 December 2024 diff hist +31‎ Unix pipes ‎ →‎stderr (Standard Error)
• 16:1116:11, 16 December 2024 diff hist +452‎ Unix pipes ‎ →‎stdin (Standard Input)
• 16:0716:07, 16 December 2024 diff hist +43‎ Unix pipes ‎ →‎stdout (Standard Output)
• 16:0516:05, 16 December 2024 diff hist +110‎ Unix pipes ‎ →‎stdin (Standard Input)
• 16:0216:02, 16 December 2024 diff hist +25‎ Unix pipes ‎ →‎stdin (Standard Input)
• 15:5815:58, 16 December 2024 diff hist +354‎ Unix pipes ‎ →‎stdout (Standard Output)
• 15:5015:50, 16 December 2024 diff hist −11‎ Unix pipes ‎ →‎stdout (Standard Output)
• 15:3715:37, 16 December 2024 diff hist −109‎ Unix pipes ‎No edit summary
• 15:3215:32, 16 December 2024 diff hist −510‎ Unix pipes ‎No edit summary

15 December 2024

• 16:2816:28, 15 December 2024 diff hist −5,305‎ SNP calling exercise part 2 answers ‎No edit summary current
• 16:2816:28, 15 December 2024 diff hist +7,265‎ N SNP calling exercise part 2 answers ‎ Created page with "'''Q1''' First, running: <pre> tabix -f -p vcf NA24694.gvcf.gz </pre> then <pre> gatk --java-options "-Xmx10g" HaplotypeCaller -R /home/databases/references/human/GRCh38_full_analysis_set_plus_decoy_hla.fa -I /home/projects/22126_NGS/exercises/snp_calling/NA24694.bam -L chr20 -O NA24694.gvcf.gz --dbsnp /home/databases/databases/GRCh38/Homo_sapiens_assembly38.dbsnp138.vcf.gz -ERC GVCF </pre> <pre> gatk GenotypeGVCFs -R /home/databases/references/human/GRCh3..."
• 16:2716:27, 15 December 2024 diff hist +3,647‎ N SNP calling exercise part 1 answers ‎ Created page with "'''Q1''' First, running: <pre> tabix -f -p vcf NA24694.gvcf.gz </pre> then <pre> gatk --java-options "-Xmx10g" HaplotypeCaller -R /home/databases/references/human/GRCh38_full_analysis_set_plus_decoy_hla.fa -I /home/projects/22126_NGS/exercises/snp_calling/NA24694.bam -L chr20 -O NA24694.gvcf.gz --dbsnp /home/databases/databases/GRCh38/Homo_sapiens_assembly38.dbsnp138.vcf.gz -ERC GVCF </pre> <pre> gatk GenotypeGVCFs -R /home/databases/references/human/GRCh3..." current
• 16:2716:27, 15 December 2024 diff hist +50‎ SNP calling exercise part 1 ‎No edit summary current
• 16:2716:27, 15 December 2024 diff hist +2‎ SNP calling exercise part 2 ‎No edit summary current
• 16:2516:25, 15 December 2024 diff hist +116‎ SNP calling exercise part 2 ‎No edit summary

10 December 2024

• 17:2017:20, 10 December 2024 diff hist +35,163‎ N Unix pipes ‎ Created page with "Welcome! This small guide contains a lot of information and examples that will help you as you start learning Linux. In addition to simple Linux commands, this tutorial also provides three Python scripts, that you can run and try out the concepts yourself. # Basic Unix Commands and Concepts This is where your journey begins! If you are new to Unix-based systems and also got used to Windows or MacOS, you really need a brief explanation of a few key commands and concept..."

29 November 2024

• 15:0615:06, 29 November 2024 diff hist +6,211‎ N SNP calling exercise part 2 ‎ Created page with " <H2> Filtering</H2> We saw that the data contains some calls of poor quality. Ideally, we do not want to carry over these calls into downstream analyses. We will explore how to filter out genotype data. <H3> Hard filtering </H3> A major downside of soft filtering is that does not apply for samples for which we do not have a good representation of the genetic diversity. An alternative is to do hard filtering meaning filtering the variants according to predetermined..."
• 14:5214:52, 29 November 2024 diff hist −975‎ SNP calling exercise answers part 1 ‎No edit summary current
• 14:3614:36, 29 November 2024 diff hist +67‎ SNP calling exercise part 1 ‎No edit summary
• 14:3514:35, 29 November 2024 diff hist +4,622‎ N SNP calling exercise answers part 1 ‎ Created page with "'''Q1''' First, running: <pre> tabix -f -p vcf NA24694.gvcf.gz </pre> then <pre> gatk --java-options "-Xmx10g" HaplotypeCaller -R /home/databases/references/human/GRCh38_full_analysis_set_plus_decoy_hla.fa -I /home/projects/22126_NGS/exercises/snp_calling/NA24694.bam -L chr20 -O NA24694.gvcf.gz --dbsnp /home/databases/databases/GRCh38/Homo_sapiens_assembly38.dbsnp138.vcf.gz -ERC GVCF </pre> <pre> gatk GenotypeGVCFs -R /home/databases/references/human/GRCh3..."
• 14:3314:33, 29 November 2024 diff hist +6,264‎ N SNP calling exercise part 1 ‎ Created page with "<H2>Overview</H2> First: <OL> <LI>Navigate to your home directory: <LI>Create a directory called "variant_call" <LI>Navigate to the directory you just created. </OL> We will: <OL> <LI>Genotype some whole-genome sequencing data. <LI>Get acquainted with VCF files <LI>Soft filtering <LI>Hard filtering <LI> Annotation of variants </OL> ---- <H2>Genotyping</H2> We will genotype a chromosome from a BAM file that has been processed using the steps we detailed before. It i..."
• 14:2714:27, 29 November 2024 diff hist +46‎ Program 2025 ‎No edit summary current
• 14:0214:02, 29 November 2024 diff hist +203‎ Denovo solution ‎No edit summary current
• 13:5513:55, 29 November 2024 diff hist +320‎ Denovo solution ‎No edit summary
• 13:5513:55, 29 November 2024 diff hist +1‎ Denovo exercise ‎No edit summary current
• 13:5513:55, 29 November 2024 diff hist +1‎ Denovo exercise ‎No edit summary
• 13:5413:54, 29 November 2024 diff hist +1,071‎ Denovo exercise ‎No edit summary
• 13:0313:03, 29 November 2024 diff hist +2‎ Denovo exercise ‎No edit summary
• 11:1611:16, 29 November 2024 diff hist +16‎ Denovo exercise ‎No edit summary

28 November 2024

• 15:4915:49, 28 November 2024 diff hist −18‎ Denovo solution ‎No edit summary
• 15:4915:49, 28 November 2024 diff hist +2‎ Denovo exercise ‎No edit summary
• 15:4615:46, 28 November 2024 diff hist +129‎ Denovo exercise ‎No edit summary
• 15:4315:43, 28 November 2024 diff hist +30‎ Denovo exercise ‎No edit summary
• 15:3915:39, 28 November 2024 diff hist +37‎ Denovo exercise ‎No edit summary
• 15:3715:37, 28 November 2024 diff hist +28‎ Denovo exercise ‎No edit summary
• 15:3615:36, 28 November 2024 diff hist +67‎ Denovo exercise ‎No edit summary