strand specific wig files

[frymor]

Hi,

I am trying to create strand-specific wig files from a bam file.
I used the pileup option and i thought it worked very good. Now I have checked it again with the mpileup and it looks very strange to me.

This is how I did it before:

samtools view -h -f 0x10 dilpAll.sorted.bam | samtools pileup -S - | cut -f 1,2,4| awk 'BEGIN{print "tracktype=\"wiggle_0\"\tname=\"dilp (reversestrand)\"\tdescription=\"dilp (reverse strand)\""} {if(NR==1){curChr=$1; print "variableStep chrom="curChr" span=1";} 
if($1 == curChr){print $2"\t"$3;}else{curChr=$1; print "curChr="curChr;}}' > wigFiles/dilp_rs.wig

samtools view -h -F 0x10 dilpAll.sorted.bam | samtools pileup -S - | cut -f 1,2,4| awk 'BEGIN{print "track type=\"wiggle_0\"\tname=\"dilp (forward strand)\"\tdescription=\"dilp (forward strand)\""} {if(NR==1){curChr=$1; print "variableStep chrom="curChr" span=1";
} if($1 == curChr){print $2"\t"$3;}else{curChr=$1; print "curChr="curChr;}}' > wigFiles/dilp_fs.wig

Now I just have changed it a bit to fit the mpileup options:

samtools view[COLOR="Red"] -b[/COLOR] -f 0x10 dilpAll.sorted.bam | samtools[COLOR="Red"] mpileup  - [/COLOR]| cut -f 1,2,4| awk 'BEGIN{print "tracktype=\"wiggle_0\"\tname=\"dilp (reversestrand)\"\tdescription=\"dilp (reverse strand)\""} {if(NR==1){curChr=$1; print "variableStep chrom="curChr" span=1";} 
if($1 == curChr){print $2"\t"$3;}else{curChr=$1; print "curChr="curChr;}}' > wigFiles/dilp_rs.wig

samtools view [COLOR="Red"]-b [/COLOR]-F 0x10 dilpAll.sorted.bam | samtools[COLOR="Red"] mpileup - [/COLOR]| cut -f 1,2,4| awk 'BEGIN{print "track type=\"wiggle_0\"\tname=\"dilp (forward strand)\"\tdescription=\"dilp (forward strand)\""} {if(NR==1){curChr=$1; print "variableStep chrom="curChr" span=1";
} if($1 == curChr){print $2"\t"$3;}else{curChr=$1; print "curChr="curChr;}}' > wigFiles/dilp_fs.wig

Than I compared it with a wig file for the omplete bam file:

samtools mpileup dilpMerged.sorted.bam | perl -ne 'BEGIN{print "track type=wiggle_0 name=fileName description=fileName\n"};($c, $start, undef, $depth) = split; if ($c ne $lastC) {print "variableStep chrom=chr$c\n"; };$lastC=$c;next unless $. % 10 ==0;print "$star
t\t$depth\n" unless $depth<3;'  > wigFiles/dilpMerged.wig

When doing it for both strands I get more line than I have together in the wig file for the complete bam file.
-f: 113905
-F: 121720
w.o.: 141199

Does someone have an explanation for these numbers?

Thanks
Assa