You may want to see this link on how to convert a SAM file (without a header) to a bam file. Afterwards you can use the BEDtool genomeCoverageBed to obtain a bedgraph file (which is similar to a wiggle file and probably will suit your needs)
Here (under software) is small sam2wig perl-script. It is not very memory efficient and/or fast, but my intention to write it was the normalization of multiple mapping reads, which cannot be done using samtools.
<p>Dear All,</p> <p>I want to change from Bowtie to Bowtie2 since Bowtie2 supportes gapped alignments. Normally I used to following command in Bowtie: </p> <pre><code>bowtie …