User contributions for Gabre
Jump to navigation
Jump to search
23 January 2025
- 10:0510:05, 23 January 2025 diff hist −7 Program 2025 No edit summary current
20 January 2025
- 09:1109:11, 20 January 2025 diff hist 0 Program 2025 No edit summary
14 January 2025
- 14:1114:11, 14 January 2025 diff hist −199 QuantitativeMetagenomics No edit summary current
- 12:1712:17, 14 January 2025 diff hist +6 Program 2025 No edit summary
- 11:2811:28, 14 January 2025 diff hist 0 Program 2025 No edit summary
13 January 2025
- 12:5712:57, 13 January 2025 diff hist +3 QuantitativeMetagenomics No edit summary
- 11:4711:47, 13 January 2025 diff hist +17 Program 2025 No edit summary
9 January 2025
- 12:2012:20, 9 January 2025 diff hist 0 Program 2025 No edit summary
- 12:1912:19, 9 January 2025 diff hist +7 Program 2025 No edit summary
- 10:5910:59, 9 January 2025 diff hist −3 Denovo exercise No edit summary current
8 January 2025
- 13:2613:26, 8 January 2025 diff hist +1,960 N SNP calling exercise answers part 2 Created page with " '''Q1''' First running: <pre> gatk VariantFiltration -V NA24694.vcf.gz -O NA24694_hf.vcf.gz -filter "DP < 10.0" --filter-name "DP" -filter "QUAL < 30.0" --filter-name "QUAL30" -filter "SOR > 3.0" --filter-name "SOR3" -filter "FS > 60.0" --filter-name "FS60" -filter "MQ < 40.0" --filter-name "MQ40" </pre> and <pre> bcftools view -H NA24694_hf.vcf.gz |grep -v PASS |wc -l </pre> Gives us 4005 sites. <pre> bcftools view -H --type=..." current
7 January 2025
- 15:4215:42, 7 January 2025 diff hist 0 Program 2025 No edit summary
- 14:3014:30, 7 January 2025 diff hist 0 Alignment exercise No edit summary current
6 January 2025
- 15:2915:29, 6 January 2025 diff hist +19 Program 2025 No edit summary
- 15:2615:26, 6 January 2025 diff hist +1 Program 2025 No edit summary
- 15:2515:25, 6 January 2025 diff hist +418 Program 2025 No edit summary
- 15:2215:22, 6 January 2025 diff hist −4 Program 2025 No edit summary
- 15:2115:21, 6 January 2025 diff hist −464 Program 2025 No edit summary
- 12:1612:16, 6 January 2025 diff hist +3 Program 2025 No edit summary
- 11:3511:35, 6 January 2025 diff hist +102 Logging on to pupil system No edit summary current
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..."