Changes between Version 6 and Version 7 of SOPs/chip_seq_peaks

Timestamp:

05/14/14 12:53:54 (11 years ago)

Author:

gbell

Comment:

--

SOPs/chip_seq_peaks

@@ -29 +29 @@
   * MACS may have trouble with a SAM file from bowtie if it contains unmapped reads (which it generally does).  As a result, you may need to filter out unmapped reads with a command like
 {{{
-samtools view -hS -F 4 s8_control_mouse_mm9.k1.n2.l36.best.sam > s8_control_mouse_mm9.k1.n2.l36.best.mapped_only.sam
+samtools view -hS -F 4 all_reads.sam > mapped_reads.sam
 }}}
 
@@ -39 +39 @@
 
 {{{
-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
-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
+macs -t IP_mapped.map -c Control_mapped.map -g 1.87e9 --name=outputName --format=BOWTIE --tsize=36 --wig --space=25  --mfold=10,30
+macs -t IP_mapped.sam -c Control_mapped.sam -g 1.87e9 --name=outputName --format=SAM    --tsize=36 --wig --space=25  --mfold=10,30
 }}}
 
@@ -55 +55 @@
 
 {{{
-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"
-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"
+bsub "macs14 -t IP_mapped.map -c Control_mapped.map --name=outputName --format=BOWTIE --tsize=36 --wig --space=25 --mfold=10,30"
+bsub "macs14 -t IP_mapped.sam -c Control_mapped.sam --name=outputName --format=SAM    --tsize=36 --wig --space=25 --mfold=10,30"
 }}}
 
@@ -68 +68 @@
 Map with Bowtie, use --sam parameter to get a sam ouput file
 {{{
-bsub "bowtie -t  -m 3 -n 3 -l 36  --strata --best --solexa1.3-quals  --sam   inputSeq bowtieOutput.sam"
+bsub "bowtie -t -m 3 -n 3 -l 36 --strata --best --solexa1.3-quals --sam inputSeq bowtieOutput.sam"
 }}}
 
@@ -74 +74 @@
 
 {{{
-bsub "samtools view  -S -b -o bowtieOutput.bam   bowtieOutput.sam" 
+bsub "samtools view -S -b -o bowtieOutput.bam bowtieOutput.sam" 
 -S       input is SAM
 -b       output BAM
@@ -85 +85 @@
 Run SISSRs with a sample command like
 {{{
-sissrs.pl -i  bowtieOutput.bed -o outputFile  -s 2716965481 -b Background.bed -L 200
+sissrs.pl -i bowtieOutput.bed -o outputFile -s 2716965481 -b Background.bed -L 200
  }}}