Changes between Version 16 and Version 17 of SOPs/mapping


Ignore:
Timestamp:
01/31/14 11:13:55 (11 years ago)
Author:
gbell
Comment:

--

Legend:

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  • SOPs/mapping

    v16 v17  
    9494Sample command:
    9595{{{
    96 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
     96bsub tophat -o s_7_tophat_out --phred64-quals --segment-length 20 -I 200000 -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
    9797}}}
    9898
    … …  
    100100  * '''-o/--output-dir <word>'''     All output files will be created in this directory (default = tophat_out)
    101101  * '''--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.
    102   * '''-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.
     102  * '''-I <int>''' Maximum intron length.  If your genome has introns that are all shorter (or many that are longer) than the default value (500000), set this to a more appropriate value.
    103103  * '''-G <GTF file>''' Supply bowtie with a GTF file of transcript models.  This can help bowtie identify functions that may otherwise be missed.
    104104  * '''--no-novel-juncs ''' Only look for spliced reads across junctions in the supplied GTF file.  Typically not used.
    … …  
    113113Sample command:
    114114{{{
    115 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
     115bsub tophat -o s_7_tophat_out --phred64-quals --segment-length 20 -I 200000 -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
    116116}}}
    117117