Changes between Version 9 and Version 10 of SOPs/mapping


Ignore:
Timestamp:
09/12/13 10:02:17 (12 years ago)
Author:
gbell
Comment:

--

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  • SOPs/mapping

    v9 v10  
    3737}}}
    3838
    39 The parameters included in the sample command are:
     39The parameters included in the sample command:
    4040  * '''-L <int>'''     length of seed substrings; must be >3 and <32 (default=22)
    4141  * '''-N <int>'''     max # mismatches in seed alignment; can be 0 or 1 (default=0)
    42   * '''--phred64'''    (if input quals are from GA Pipeline ver. >= 1.3 and before Illumina 1.8)  See the table at the top of FastQC output to identify the "encoding" scale [[br]]
    4342  * '''-S'''           name of SAM output file
     43Choices for fastq encoding (which is listed as "Encoding" in the top "Basic Statistics" table of the FastQC output file).  See the [http://en.wikipedia.org/wiki/FASTQ_format FASTQ format page] for more details.
     44  * '''--solexa-quals'''         (for input quality scores from Illumina versions 1.2 and earlier)
     45  * '''--phred64'''     (for input quality scores from Illumina versions 1.3-1.7)
     46  * '''--phred33'''         (default "Sanger format"; for input quality scores from Illumina versions 1.8 and later)
    4447
    4548bowtie2 can also perform local alignments where the unaligned end(s) of a read are clipped (so, for example, remaining adapter won't prevent alignment) by adding the argument '''--local'''.
    … …  
    6669Sample command:
    6770{{{
    68 bsub tophat -o s_7_tophat_out --phred64-quals --no-novel-juncs --segment-length 20 -G /nfs/genomes/mouse_gp_jul_07_no_random/gtf/Mus_musculus.NCBIM37.67_noNT.gtf /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt
     71bsub tophat -o s_7_tophat_out --phred64-quals --segment-length 20 -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
    6972}}}
    7073
    7174The parameters included in the sample command are:
    7275  * '''-o/--output-dir <word>'''     All output files will be created in this directory (default = tophat_out)
    73   * '''--solexa-quals'''             (if input quals are from GA Pipeline ver. < 1.3)  See the table at the top of FastQC output to identify the "encoding" scale [[br]]
    74   * '''--phred64-quals''' or '''solexa1.3-quals'''   (if input quals are from GA Pipeline ver. >= 1.3 before Illumina 1.8)  See the table at the top of FastQC output to identify the "encoding" scale [[br]]
     76  * '''--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  * '''-G <GTF file>''' Supply bowtie with a GTF file of transcript models.  This can help bowtie identify functions that may otherwise be missed.
     78  * '''--no-novel-juncs ''' Only look for spliced reads across junctions in the supplied GTF file.  Typically not used.
     79Choices for fastq encoding (which is listed as "Encoding" in the top "Basic Statistics" table of the FastQC output file).  See the [http://en.wikipedia.org/wiki/FASTQ_format FASTQ format page] for more details.
     80  * '''--solexa-quals'''         (for input quality scores from Illumina versions 1.2 and earlier)
     81  * '''--solexa1.3-quals''' or '''--phred64-quals'''     (for input quality scores from Illumina versions 1.3-1.7)
     82
     83'''[http://tophat.cbcb.umd.edu/ tophat version 2]'''
     84
     85TopHat version 2 uses bowtie2, rather than bowtie, for its mapping.
     86
     87Sample command:
     88{{{
     89bsub tophat -o s_7_tophat_out --phred64-quals --segment-length 20 -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
     90}}}
     91
     92The parameters included in the sample command are:
     93  * '''-o/--output-dir <word>'''     All output files will be created in this directory (default = tophat_out)
     94  * '''--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.
     95  * '''-G <GTF file>''' Supply bowtie with a GTF file of transcript models.  This can help bowtie identify functions that may otherwise be missed.
     96  * '''--no-novel-juncs ''' Only look for spliced reads across junctions in the supplied GTF file.  Typically not used.
     97
     98Choices for fastq encoding (which is listed as "Encoding" in the top "Basic Statistics" table of the FastQC output file).  See the [http://en.wikipedia.org/wiki/FASTQ_format FASTQ format page] for more details.
     99  * '''--solexa-quals'''         (for input quality scores from Illumina versions 1.2 and earlier)
     100  * '''--solexa1.3-quals''' or '''--phred64-quals'''     (for input quality scores from Illumina versions 1.3-1.7)
     101