Hi everybody,

I have found an old description of how to convert a bam file into wig using perl.

(How can I convert BAM/SAM to wiggle).

In this example (as far as I understood it) the whole bam file was converted.

samtools pileup bam_small.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 $. % 10 ==0;print "$start\t$depth\n" unless $depth<3;' \
 > fileName1.wig

This command works just fine for single or multiple chromosomes.

Now I wanted to change the command to make a strand-specific wig file for forward and reverse strands, so I tried to tweak the command a bit. AS pileup is deprecated, I used mpileup:

samtools view -h -f 0x10 bam_small.sorted.bam |\
samtools mpileup -S -  |\
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 $. % 10 ==0;print "$start\t$depth\n" unless $depth<3;' \
> fileName1.wig

The 0x10 flag is used for the strand of the query, but somehow it doesn't work. I keep getting this error massage:

[bam_header_read] invalid BAM binary header (this is not a BAM file).

Does anyone has an idea how to run this command?

Thanks

Assa