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- sorted.bam SORT_ORDER=coordinate java -jar /home/groups/schumer/shared_bin/BuildBamIndex.jar INPUT=file.sorted.bam 3) mark read duplicates in the bam file...102 KB (14,283 words) - 14:09, 31 May 2024
- 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) - 07:18, 27 September 2017
- 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...41 KB (4,103 words) - 13:08, 16 January 2024
- list, feel free to add more. HindIII (wasn't able to remove from Bba_P1001), BamHI, XhoI, NcoI (wasn't able to remove from I50000, pSB5** series plamids),...13 KB (1,603 words) - 03:53, 1 July 2012
- telecommunication) are time base media How to look at the world through nature’s point of view? How can artwork change itself during a show? How can artwork change as it...6 KB (562 words) - 11:21, 24 December 2009
- 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 (3,053 words) - 01:48, 20 September 2014
- 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 (600 words) - 01:58, 18 June 2010
- 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) - 08:23, 2 June 2010
- 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 (4,166 words) - 10:56, 11 September 2014
- 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) - 00:49, 9 June 2010
- 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) - 20:29, 12 January 2019
- 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 (199 words) - 15:25, 3 September 2007
- 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
- is the Eco/Bam transfer for the lacZ gene. Construction files: 1) Part sbb1111 {P_oppBCF} PCR ss36f/ss36r on MG1655 gen. (1519bp, EcoRI/BamHI) Sub into...7 KB (1,025 words) - 11:33, 10 March 2011
- Example: samtools merge /data/males.bam /data/002Maligned.bam /data/006Maligned.bam /data/029Maligned.bam /data/113Maligned.bam Methylation calling using BS-Seeker2...39 KB (4,567 words) - 08:27, 22 August 2017
- 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) - 11:00, 10 March 2011
- <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 (468 words) - 09:24, 11 September 2007
- reads_vs_my_genome_db.sam To convert it to bam format use samtools: samtools view -but my_genome.fasta.fai -o reads_vs_my_genome_db.unsorted.bam reads_vs_my_genome_db.sam...12 KB (1,677 words) - 02:50, 30 September 2014
- 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 (3,925 words) - 16:54, 13 September 2007
- 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 (4,981 words) - 09:07, 16 February 2007
