Changes between Version 5 and Version 6 of SOPs/mapping


Ignore:
Timestamp:
06/12/13 13:24:46 (12 years ago)
Author:
gbell
Comment:

--

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  • SOPs/mapping

    v5 v6  
    1313Sample command:
    1414{{{
    15 bsub "bowtie  -k 1 -n 2 -l 70 --best --sam --solexa1.3-quals /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt s7_mm9.k1.n2.l36.best.sam"
     15bsub bowtie  -k 1 -n 2 -l 70 --best --sam --solexa1.3-quals /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt s7_mm9.k1.n2.l36.best.sam
    1616}}}
    1717
    18 The parameters used on the sample command are:
     18The parameters included in the sample command are:
    1919  * '''-l/--seedlen <int>'''     seed length for -n (default: 28) -- Set to longest possible length of high-quality bases.  Use the FastQC output to determine length of high-quality positions.
    2020  * '''-n/--seedmms <int>'''     max mismatches in seed (can be 0-3, default: -n 2)
    … …  
    3131Sample command:
    3232{{{
    33 bsub "bsub bowtie2 --phred64 -L 22 -N 1 -x /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt -S s7_mm9.L22.N1.sam"
     33bsub bsub bowtie2 --phred64 -L 22 -N 1 -x /nfs/genomes/mouse_gp_jul_07_no_random/bowtie/mm9 s_7.txt -S s7_mm9.L22.N1.sam
    3434}}}
    3535
    36 The parameters used on the sample command are:
     36The parameters included in the sample command are:
    3737  * '''-L <int>'''     length of seed substrings; must be >3 and <32 (default=22)
    3838  * '''-N <int>'''     max # mismatches in seed alignment; can be 0 or 1 (default=0)
    … …  
    4242bowtie2 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'''.
    4343
     44'''Other tools'''
    4445
     46Many other regular mapping tools are also available, although they generally require a tool-specific indexed version of the genome.
    4547
    4648== Splice-aware mappers ==
     49
     50These mappers permit the beginning and end of a read to map to (originate from) different places in the genome, which is common for spliced RNA.
     51
     52'''[http://tophat.cbcb.umd.edu/ tophat version 1]'''
     53
     54Running TopHat version 1 requires a change to a user's environment on tak (and only applies to the specific tak session.  First run this command:
     55{{{
     56export PATH="/usr/local/share/tophat1:$PATH"
     57}}}
     58and then check that your terminal will use the correct TopHat version:
     59{{{
     60tophat --version
     61}}}
     62
     63Sample command:
     64{{{
     65bsub 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
     66}}}
     67
     68The parameters included in the sample command are:
     69  * '''-o/--output-dir <word>'''     All output files will be created in this directory (default = tophat_out)
     70  * '''--phred64-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]]