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- to sort bam files by read names, and converted back to fastq files using bedtools bamToFastq). To upload your data, you can access our file server named...15 KB (1,174 words) - 14:40, 25 October 2023
- bedtools is an incredibly useful program for overlap files of many common format types. Check out the bedtools documentation here [[1]] Here are some examples...7 KB (913 words) - 10:17, 2 November 2023
- ki-bmc/pipeline_1.2 snpeff/2.0.5d bedtools/2.15.0(default) cufflinks/2.0.1 ki-bmc/pipeline_1.2.1 snpsnift/1.3.4b bedtools/2.16.1 cufflinks/2.0.2 materialsstudio/6...9 KB (1,186 words) - 11:07, 14 December 2022
- Wikiomics:WinterSchool day2 (section bedtools)ensembl.txt to ref_gen.fa Annotations: #bed file with just one line used for bedtools intersect 1 48850000 49020000 Getting the FASTQ files containing reads...25 KB (4,166 words) - 10:56, 11 September 2014
- the wiki Gene discovery and annotation Variant calling SAMtools Picard bedtools GATK (but also check out their community site) snpEff FreeBayes Syzygy...4 KB (0 words) - 16:41, 23 September 2017
- environment. fastxtoolkit (confirmed for v0.0.13) bowtie2 (confirmed for v2.2.3) bedtools (confirmed for v2.20.1) r (confirmed for v2.15.3) perl (confirmed for v5...4 KB (514 words) - 05:19, 16 June 2016
- samtools, and bedtools fastqc upgraded from 0.11.2 to 0.11.4 bwa upgraded from 0.7.10 to 0.7.12 samtools upgraded from 0.1.19 to 1.3 bedtools upgraded from...13 KB (1,993 words) - 08:21, 14 December 2022
- added or updated on ROUS in the past few months: trinityrnaseq: r20140413p1 bedtools: 2.20.1 bowtie2: 2.2.3 tophat: 2.0.12 rsem: 1.2.15 fastqc: 0.11.2 bwa:...8 KB (1,142 words) - 09:30, 3 January 2017
- fastqc which is installed on sirius) Top Wayne Lab Home Top Wayne Lab Home BEDtools SAMtools Top Wayne Lab Home GATK and GATK Guide Top Wayne Lab Home Here...19 KB (2,211 words) - 12:56, 29 May 2013
- calculate_features_per_window.R bins.bed features.gtf_or_features.bed path_to_bedtools_bin/[0 for global install] outfile_name for example: Rscript calculate...32 KB (4,368 words) - 15:10, 8 June 2023
- trimming/clipping QC FASTX toolkit Lab Home Lab Meeting Laboratory Protocols BEDtools SAMtools samtools can also be used for making pileups, calling variants...39 KB (4,567 words) - 08:27, 22 August 2017
- the reference can be replaced with the haplotype (e.g. using seqkit or bedtools). X or Y can be identified based on homology to other species. These scaffolds...102 KB (14,283 words) - 14:09, 31 May 2024
- form, BAM files. The few used on daily/basis: samtools Picard bamtools bedtools Typical tasks: #view the BAM file samtools view your_bam | less #view the...32 KB (5,232 words) - 09:36, 22 September 2014
