Changes between Version 14 and Version 15 of SOPs/mapping
- Timestamp:
- 01/15/14 14:14:51 (11 years ago)
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SOPs/mapping
v14 v15 32 32 '''[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml bowtie version 2]''' 33 33 34 Bowtie 2 was designed as an improvement to bowtie 1. See the first [http://bowtie-bio.sourceforge.net/bowtie2/faq.shtml bowtie2 FAQ] for how they differ. Early versions of bowtie 2 had some issues, but these seem to have been fixed. Bowtie 2 uses a different set of genome index files (*.bt2) than bowtie 1 (*.ebwt). 34 Bowtie 2 was designed as an improvement to bowtie 1. See the first [http://bowtie-bio.sourceforge.net/bowtie2/faq.shtml bowtie2 FAQ] for how they differ. Early versions of bowtie 2 had some issues, but these seem to have been fixed. Bowtie 2 uses a different set of genome index files (*.bt2) than bowtie 1 (*.ebwt). Bowtie 2 works with indels. 35 35 36 36 Sample command: … … 54 54 Bwa is a software package containing several related algorithms using the Burrows-Wheeler Transform. It works well even with indels, but not with spliced (RNA) reads. 55 55 56 Sample commands for s ort (<70 nt) reads:56 Sample commands for short (<=100 nt) reads: 57 57 {{{ 58 # Align single reads58 # Align single-end reads 59 59 bsub "bwa aln /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9 Reads.fq > Mapped_reads.sai" 60 60 bsub "bwa samse /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9 Mapped_reads.sai Reads.fq > Reads.bwa.sam" … … 67 67 Sample commands for long (70 nt - 1M nt) reads: 68 68 {{{ 69 # Align single reads69 # Align single-end reads 70 70 bsub "bwa mem /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9 Reads.fq > Mapped_reads.bwa.sam" 71 71 # Align paired-end reads