bowtie assembly on RNA seq viewer

[jjk]

Hello,

Just did a bowtie assembly on RNAseq data, checked in tablet all looks fine but is there a way to find out the coverage for each nucleotide in the genome file?

Thanks,

[jjk]

Reply to anyone who has found this through searching and was facing the same problem

Generating bam file
~/Apps/samtools-0.1.18/samtools view -bS xxx.sam > xxx.bam

Sorting
~/Apps/samtools-0.1.18/samtools sort xxx.bam xxx-sorted.bam

Indexing
~/Apps/samtools-0.1.18/samtools index xxx.bam

Viewing

BamView, open sorted file (make sure that the index bam.bai file is there) generated by indexing
Open the FASTA file for reference

Go!