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- Etchevers:Notebook/STRA6 in eye development/2009/06/29 (section Linux running Maq for a 3-day weekend)For SOX2: ~$ cd maq-0.7.1 ~/maq-0.7.1$ maq.pl easyrun -d outdirSOX2 refhg19.fasta GDZ_SOX2.fastq -- CMD: xx/maq-0.7.1/maq fasta2bfa xx/maq-0.7.1/refhg19...12 KB (0 words) - 17:10, 26 September 2017
- chunks of 1 million PE reads ← Fix this! why? foreach fastq file : maq fastq2bfq $fq $bfq maq map -e 70 -a max_insert_size_for_lane -u $unmapped $mapped $bfa...886 bytes (117 words) - 08:23, 2 June 2010
- heather@heather-desktop:~/maq-0.7.1$ maq.pl easyrun -d outdir refhg19.fasta GDZ1_OTX2.fastq -- CMD: /home/heather/maq-0.7.1/maq fasta2bfa /home/heather/maq-0.7.1/refhg19...9 KB (0 words) - 17:09, 26 September 2017
- PAX6-FP -input ~/maq-0.7.1/outdirPAX6/allPAX6.map -output ~/maq-0.7.1/FindPeaksResults/ -maq_read_size 128 -qualityfilter 10 -aligner maq -one_per -saturation...3 KB (0 words) - 17:11, 26 September 2017
- tion_pipeline/Reference_genome SAMTOOLS http://samtools.sourceforge.net/ MAQ BWA Mapping quality =30 = GOOD Mapping quality is p(alignment is incorrect)*...5 KB (600 words) - 01:58, 18 June 2010
- fa | grep -v _hap | xargs cat > hg18.fa rm -f chr*.fa (main article for MAQ). maq fasta2bfa hg18.fa hg18.bfa (...) -- 45 sequences have been converted ls...2 KB (309 words) - 08:27, 2 June 2010
- Orchestra /groups/pgp/ PGP4 now available process data with GAP1.3.2, Swift, MAQ BOINC application read documentation, download and use correspond with David...4 KB (11 words) - 13:15, 30 November 2009
- PAX6-FP -input ~/maq-0.7.1/outdirPAX6/allPAX6.map -output ~/maq-0.7.1/FindPeaksResults/ -maq_read_size 128 -qualityfilter 10 -aligner maq -one_per -saturation...9 KB (0 words) - 17:10, 26 September 2017
- development Main project page Previous entry Next entry Managed to compile the MAQ program. First after having installed Jaunty Jackalope Ubuntu 9.04 I had to...3 KB (0 words) - 17:09, 26 September 2017
- input fragments and deep sequence coverage. ALLPATHS (HTML) algorithm only Maq mapping short reads to an existing genomic sequence SOAP suite of programs...4 KB (436 words) - 15:34, 12 February 2010
- trunk/src/projects/maq_utilities A trunk/src/projects/maq_utilities/ReadsUsed.java A trunk/src/projects/maq_utilities/objects A trunk/src/projects/maq_utilities...15 KB (0 words) - 17:32, 26 September 2017
- directory I made, for OTX2-1 [GDZ-1 for Fasteris]. The log for OTX2-1 is: - maq-0.7.1 [ma_load_reads] loading reads... [ma_load_reads] set length of the first...8 KB (0 words) - 17:09, 26 September 2017
- create improved versions of ELAND. Some of the options: MAQ http://maq.sourceforge.net/ - Maq maps short reads to a reference genome and calls the genotypes...16 KB (2,406 words) - 12:14, 13 January 2011
- trunk/src/projects/maq_utilities trunk/src/projects/maq_utilities/ReadsUsed.java trunk/src/projects/maq_utilities/objects trunk/src/projects/maq_utilities/ob...15 KB (0 words) - 17:11, 26 September 2017
- post-processing of YASRA contigs. SOAP - Short Oligonucleotide Analysis Package. MAQ - Mapping and Assembly with Qualities. Bowtie - Bowtie. An ultrafast, memory-efficient...5 KB (461 words) - 13:17, 20 June 2012
- sort output.bam sorted_prefix do insert size stats e.g. 99.8 percentile for MAQ max insert size ← Fix this! what does that mean ?...1 KB (180 words) - 00:49, 9 June 2010
- of RNA-seq data. When we have a reasonable reference we use either RGA or MAQ. Short read toolbox...2 KB (235 words) - 23:23, 12 September 2011
- - Utilizes quality scores. SOAP - Short Oligonucleotide Analysis Package. MAQ - Mapping and Assembly with Qualities. Bowtie - Bowtie. An ultrafast, memory-efficient...8 KB (647 words) - 17:46, 5 June 2012
- Deliverables: Illumina files containing the sequence information, and PGP MAQ pipeline-generated results are here for download. (here). Publications on...5 KB (11 words) - 13:35, 23 December 2008
- /home/trait/core/json_to_job_database.py /home/trait/core/maq_snp_to_gff.py - outputs GFF record for each entry in a Maq SNP file /home/trait/core/omim_print_variants...13 KB (2,048 words) - 21:08, 10 December 2009
