Changes between Version 7 and Version 8 of SOPs/InProgressChipSeq


Ignore:
Timestamp:
05/14/14 16:04:35 (10 years ago)
Author:
ibarrasa
Comment:

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Legend:

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  • SOPs/InProgressChipSeq

    v7 v8  
    4646
    4747Sample commands to run MACS (current version as of March 5 2012): 1.4.2 using mapped reads in map or sam format:
    48 
    49 {{{
    50 macs -t ./s7_mouse_mm9.k1.n2.l36.best.map -c ./s8_control_mouse_mm9.k1.n2.l36.best.map -g 1.87e9 --name=outputName --format=BOWTIE --tsize=36 --wig --space=25  --mfold=10,30
    51 macs -t ./s7_mouse_mm9.k1.n2.l36.best.sam -c ./s8_control_mouse_mm9.k1.n2.l36.best.sam -g 1.87e9 --name=outputName --format=SAM --tsize=36 --wig --space=25  --mfold=10,30
    52 macs -t ./s7_mouse_mm9.k1.n2.l36.best.sam -c ./s8_control_mouse_mm9.k1.n2.l36.best.sam -g 1.87e9 --name=outputName --format=SAM --tsize=36 --wig --space=25 --nomodel --shiftsize=100
    53 
    54 }}}
     48{{{
     49macs -t IP_mapped.map -c Control_mapped.map -g 1.87e9 --name=outputName --format=BOWTIE --tsize=36 --wig --space=25  --mfold=10,30
     50macs -t IP_mapped.sam -c Control_mapped.sam -g 1.87e9 --name=outputName --format=SAM    --tsize=36 --wig --space=25  --mfold=10,30
     51macs -t IP_mapped.sam -c Control_mapped.sam -g 1.87e9 --name=outputName --format=SAM    --tsize=36 --wig --space=25  --nomodel --shiftsize=100
     52}}}
     53
    5554
    5655The parameters used on the command are:
    … …  
    6867
    6968{{{
    70 bsub "macs14 -t ./s7_mouse_mm9.k1.n2.l36.best.map -c ./s8_control_mouse_mm9.k1.n2.l36.best.map --name=outputName --format=BOWTIE --tsize=36 --wig --space=25  --mfold=10,30"
    71 bsub "macs14 -t ./s7_mouse_mm9.k1.n2.l36.best.sam -c ./s8_control_mouse_mm9.k1.n2.l36.best.sam --name=outputName --format=SAM--tsize=36 --wig --space=25  --mfold=10,30"
    72 }}}
     69bsub "macs14 -t IP_mapped.map -c Control_mapped.map --name=outputName --format=BOWTIE --tsize=36 --wig --space=25 --mfold=10,30"
     70bsub "macs14 -t IP_mapped.sam -c Control_mapped.sam --name=outputName --format=SAM    --tsize=36 --wig --space=25 --mfold=10,30"
     71}}}
     72
    7373
    7474''Note'': The wig files that macs14 generates are not normalized.
    … …  
    9090SISSRs uses strand bimodality to try to find the summit of the peak. The summit should be very close to the DNA bound by the TF.  It is more appropriate for TFs because they tend to bind in specific narrow regions.
    9191
    92 Map with Bowtie, use --sam parameter to get a sam ouput file
    93 {{{
    94 bsub "bowtie -t  -m 3 -n 3 -l 36  --strata --best --solexa1.3-quals  --sam  inputSeq bowtieOutput.sam"
     92Map with Bowtie, use --sam parameter to get a SAM output file
     93{{{
     94bsub "bowtie -t -m 3 -n 3 -l 36 --strata --best --solexa1.3-quals --sam inputSeq bowtieOutput.sam"
    9595}}}
    9696
    … …  
    9898
    9999{{{
    100 bsub "samtools view  -S -b -o bowtieOutput.bam  bowtieOutput.sam"
     100bsub "samtools view -S -b -o bowtieOutput.bam bowtieOutput.sam"
    101101-S       input is SAM
    102102-b       output BAM
    … …  
    109109Run SISSRs with a sample command like
    110110{{{
    111 sissrs.pl -i  bowtieOutput.bed -o outputFile -s 2716965481 -b Background.bed -L 200
     111sissrs.pl -i bowtieOutput.bed -o outputFile -s 2716965481 -b Background.bed -L 200
    112112 }}}
    113113