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- samtools creating BAM samtools view -but Lmex_genome.fa.fai Lmaj_genome_v_Lmex80.lst475.sam -o Lmaj_genome_v_Lmex80.lst475.us.bam #sort BAM samtools sort ...18 KB (3,066 words) - 08:48, 20 September 2014
- samtools view $unmapped.sam > $unmapped.bam samtools view $mapped > $mapped.bam ← Fix this! what shall we do with unmapped ? look for indels ? merge @bam using...886 bytes (117 words) - 15:23, 2 June 2010
- DNA through Nested PCR, which allowed them to add cut sites for EcoR1 and BamH1 in the env primers. Amplified DNA cloned into pUC19 vector, then sequenced...12 KB (2,005 words) - 08:00, 6 February 2020
- samtools sort unsorted_input.bam sorted_output #notice no bam suffix!!! samtools index sorted_output.bam #creates sorted_output.bam.bai We can easily calculate...25 KB (4,197 words) - 17:56, 11 September 2014
- Butlin:Unix for Bioinformatics - advanced tutorial (section TASK 8: I have just mapped my reads against the reference sequences and I got a BAM file for each individual. How can I find out the proportion of reads from each individual that got mapped successfully?)directory: $ mkdir BAM Now, let's get parallel: $ parallel "bowtie2 -x bowtie_reference_seq -U {} | samtools view -bq 1 - > BAM/{/.}.bam" ::: ind_seqs/*fq...33 KB (4,704 words) - 14:18, 27 September 2017
- fai output.sam output.bam samtools sort output.bam output.bam.sorted samtools index chr1.sorted.bam sort bam samtools sort output.bam sorted_prefix do insert...1 KB (180 words) - 07:49, 9 June 2010
- 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 (5,258 words) - 16:36, 22 September 2014
- warning BAM=${FASTQ}\_2_${REF_GENOME}_sorted.bam BAM_PREFIX=${BAM%%.bam} echo ${BAM_PREFIX} longshot --bam ${BAM} --ref ${REF_GENOME} --out ${BAM_PREFIX}...106 KB (14,834 words) - 23:47, 6 February 2025
- <calendar> name=iGEM:IMPERIAL/2007/Notebook date=2007/09/24 view=threemonths format=%name/%year-%month-%day weekstart=7 </calendar> Minipreped the 5 overnight...7 KB (469 words) - 16:24, 11 September 2007
- Fix this! command line java -jar MarkDuplicates.jar I=chr1.sorted.bam O=chr.markdup.bam METRICS_FILE=jeter.metrics ← Fix this! With GATK ? ← Fix this! 'min...5 KB (602 words) - 08:58, 18 June 2010
- have defined the functionally relevant parts; structural data gives us a view of the phage particle and its components. Together these provide detailed...25 KB (3,926 words) - 23:54, 13 September 2007
- 4 for sequencing after viewing Analytical Gel. Ligated and transformed the cut-and-paste part jtk2914 using Ligation of EcoRI/BamHI digestts and Transformation...5 KB (704 words) - 18:00, 10 March 2011
- several researchers at UC Berkeley and is based on idempotent assembly with BamHI and BglII restriction enzymes. In a nutshell, most plasmids look like this:...19 KB (1,680 words) - 09:12, 17 April 2012
- stranded BamHI tail so there will be an overhang that can anneal to the M13 genome backbone you are digesting. Bottom strand, step 3: Destroy the BamHI site...32 KB (4,982 words) - 16:07, 16 February 2007
- in terms of finding relevant articles. The ability to go to an article and view articles which had cited the original makes it very easy to find more recent...21 KB (3,030 words) - 19:58, 15 September 2014
- Benchling, or SnapGene. ApE (A Plasmid Editor) is a free software tool for viewing, annotating, and editing sequence files. To use it, you will first download...2 KB (273 words) - 20:37, 10 March 2025
- module load samtools samtools depth my_bam_file | awk '{sum+=$3} END { print sum/NR}' samtools view -c -F 260 my_bam_file...3 KB (266 words) - 03:29, 13 January 2019
- searching for dUTPase which leads to a result screen Next shows an easier way to view the abstracts of the all the search results allowing comparison making it...11 KB (1,897 words) - 04:57, 8 February 2010
- insert and vector DNA (5 μl insert/ 15 μl vector) Nde 0.75 μl BamH1 0.75 μl 10X BSA 2 μl 10X BamH1 Buffer 2 μl ddH20 to make up total volume of 20 μl Digestion...1 KB (200 words) - 22:25, 3 September 2007
- there? You may be thinking why don't we just do BamHI and BglII. Well, there's a problem with that. BamHI and BglII are specifically used for BglBricks...25 KB (3,854 words) - 15:29, 1 March 2009
