Changes between Version 11 and Version 12 of SOPs/mapping
- Timestamp:
- 09/12/13 10:20:18 (11 years ago)
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SOPs/mapping
v11 v12 31 31 32 32 '''[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml bowtie version 2]''' 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). 33 35 34 36 Sample command: … … 69 71 Sample command: 70 72 {{{ 71 bsub tophat -o s_7_tophat_out --phred64-quals --segment-length 20 -I 15000 -G /nfs/genomes/mouse_gp_jul_07_no_random/gtf/Mus_musculus.NCBIM37.67_noNT.gtf --no-novel-juncs /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt73 bsub tophat -o s_7_tophat_out --phred64-quals --segment-length 20 -I 800000 -G /nfs/genomes/mouse_gp_jul_07_no_random/gtf/Mus_musculus.NCBIM37.67_noNT.gtf --no-novel-juncs /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt 72 74 }}} 73 75 … … 75 77 * '''-o/--output-dir <word>''' All output files will be created in this directory (default = tophat_out) 76 78 * '''--segment-length <int>''' Shortest length of a spliced read that can map to one side of the junction. For reads shorter than ~45 nt, set this to half the read length (so set '--segment-length 20' for 40-nt reads). For longer reads, the default length (25) can be used. 77 * '''-I <int>''' Maximum intron length. If your genome has introns that are shorter than the default value (500000), set this to a more appropriate value (and prevent some aberrant mapping)79 * '''-I <int>''' Maximum intron length. If your genome has introns that are all shorter (or often longer) than the default value (500000), set this to a more appropriate value 78 80 * '''-G <GTF file>''' Supply bowtie with a GTF file of transcript models. This can help bowtie identify functions that may otherwise be missed. 79 81 * '''--no-novel-juncs ''' Only look for spliced reads across junctions in the supplied GTF file. Typically not used. … … 84 86 '''[http://tophat.cbcb.umd.edu/ tophat version 2]''' 85 87 86 TopHat version 2 uses bowtie2, rather than bowtie, for its mapping. 88 TopHat version 2 uses bowtie2, rather than bowtie, for its mapping. As a result, TopHat 2 uses a different set of genome index files (*.bt2) than TopHat 1 (*.ebwt). 87 89 88 90 Sample command: 89 91 {{{ 90 bsub tophat -o s_7_tophat_out --phred64-quals --segment-length 20 -I 15000 -G /nfs/genomes/mouse_gp_jul_07_no_random/gtf/Mus_musculus.NCBIM37.67_noNT.gtf --no-novel-juncs /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt92 bsub tophat -o s_7_tophat_out --phred64-quals --segment-length 20 -I 800000 -G /nfs/genomes/mouse_gp_jul_07_no_random/gtf/Mus_musculus.NCBIM37.67_noNT.gtf --no-novel-juncs /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt 91 93 }}} 92 94 … … 94 96 * '''-o/--output-dir <word>''' All output files will be created in this directory (default = tophat_out) 95 97 * '''--segment-length <int>''' Shortest length of a spliced read that can map to one side of the junction. For reads shorter than ~45 nt, set this to half the read length (so set '--segment-length 20' for 40-nt reads). For longer reads, the default length (25) can be used. 96 * '''-I <int>''' Maximum intron length. If your genome has introns that are shorter than the default value (500000), set this to a more appropriate value (and prevent some aberrant mapping)98 * '''-I <int>''' Maximum intron length. If your genome has introns that are all shorter (or often longer) than the default value (500000), set this to a more appropriate value 97 99 * '''-G <GTF file>''' Supply bowtie with a GTF file of transcript models. This can help bowtie identify functions that may otherwise be missed. 98 100 * '''--no-novel-juncs ''' Only look for spliced reads across junctions in the supplied GTF file. Typically not used.
