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- source code for some of the bioinformatics scripts used by the Liston Lab. Most of the scripts are written in Python 2.6.4 and are designed for Unix systems...9 KB (338 words) - 17:07, 22 September 2010
- File:Fly.merged.fasta Infernal Aligned reads and sequences Left half Media:Infernal_aligned_reads.left.fa.zip Right half Media:Infernal_aligned_reads.right.fa...5 KB (661 words) - 16:15, 12 July 2010
- sam reads_vs_my_genome_db.maf > 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...12 KB (1,677 words) - 02:50, 30 September 2014
- sequencing company sent you HiFi reads (CCS reads Q>20) and not CCS reads (CCS reads Q>0). Note: in the most recent update, fastq.gz read QV is no longer equivalent...102 KB (14,283 words) - 14:09, 31 May 2024
- Workflow has been completely packaged. Has been modulated. Input is raw Fasta file of reads. Output [sequences homologous to rRNA, alignments of homologous sequences...3 KB (452 words) - 13:53, 16 August 2017
- the binary fasta format maq fastq2bfq reads.fastq reads-1.bfq Convert the reads to the binary fastq format maq match reads-1.map ref.bfa reads-1.bfq Align...9 KB (0 words) - 17:09, 26 September 2017
- 100K of reads is enough: head -400000 my_reads.fastq > 100K_head_my_reads.fastq fastqc 100K_head_my_reads.fastq #we got here 100K_head_my_reads.fastq_fastqc/...32 KB (5,232 words) - 09:36, 22 September 2014
- powerful algorithm for searching for alignments between sequences of varying levels of divergence. It is most efficient for search for one of a few sequences...7 KB (913 words) - 10:17, 2 November 2023
- Butlin:Unix for Bioinformatics - advanced tutorial (section TASK 10: I have a large table from the output of the programme stacks containing the condensed information for each reference tag. Each column is tab delimited. The first column contains the tag ids. Another column the reference sequence for the tag. How can I create a multi-fasta file from this table with the tag ids as fasta headers?)stands for the base before the @ sign, \2 stands for the base after the @ sign. Finally, let’s search for the microsats: $ tr '\n' '@' < multi_fasta.fa |...33 KB (4,704 words) - 07:18, 27 September 2017
- Wikiomics:Repeat finding (section Input Reads)the input size for testing (265Mb fasta with 592k 454 reads) which is small enough. Possibly running ReAS with reas_all.pl -read input.fasta -n 8 may fix...12 KB (1,610 words) - 05:06, 2 December 2010
- divideConquerParser.sh 4 "reads_R1_allanes_combined.fastq.gz reads_R2_allanes_combined.fastq.gz reads_I1_allanes_combined.fastq.gz reads_I2_allanes_combined...32 KB (4,368 words) - 15:10, 8 June 2023
- 100K of reads is enough: head -400000 my_reads.fastq > 100K_head_my_reads.fastq fastqc 100K_head_my_reads.fastq #we got here 100K_head_my_reads.fastq_fastqc/...44 KB (7,298 words) - 08:55, 27 November 2013
- Etchevers:Notebook/STRA6 in eye development/2009/06/29 (section Linux running Maq for a 3-day weekend)(SE) reads: 3786087 -- # mapped SE reads: 3267657 (/ 3786087 = 86.3%) -- # paired end (PE) reads: 0 -- # mapped PE reads: 0 (/ 0 = NA%) -- # reads that...12 KB (0 words) - 17:10, 26 September 2017
- end reads using MEM algorithm bwa mem ref.bwa_is reads.fq > reads.bwa_mem.sam #mapping paired end reads using MEM algorithm bwa mem ref.bwa_is reads_1.fq...18 KB (3,053 words) - 01:48, 20 September 2014
- end reads using MEM algorithm bwa mem ref.bwa_is reads.fq > reads.bwa_mem.sam #mapping paired end reads using MEM algorithm bwa mem ref.bwa_is reads_1.fq...25 KB (4,166 words) - 10:56, 11 September 2014
- represented by the final sample of reads. Binary parameter for the filtering of reads: The reads that match the AMPHORA profile for the gene are then filtered...9 KB (1,514 words) - 15:20, 17 August 2017
- results: only with reads vs. with reference sequences (in two ways) reference tree helps to parcel out reads, without it the reads get lumped could be...1 KB (202 words) - 14:50, 17 August 2017
- 15 -t 10 -foutput2.aln hg18.fasta file2.fastq.gz Generate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randomly...1 KB (180 words) - 00:49, 9 June 2010
- some step by step guidance for this primer’s design but be sure to rely on your partner for help since there is no substitute for a second pair of eyes to...26 KB (3,501 words) - 17:58, 9 February 2006
- containing metagenomic reads identified by AMPHORA mg_treebuild_script.sh script to infer phylogenetic relationships among metagenomic reads mgr_treebuild_script...3 KB (504 words) - 15:23, 17 August 2017