visualising the alignment between reads and its template

[vpi]

Hi,

I want to align my reads to the desired template and look at the alignment (the sequence). I tried IGV, but It could only give me the quality of the reads but not the sequence alignment. Also tried seqmonk, which dint help much.

Could someone please suggest me a tool to look at the alignment. My templates are in fasta format and my reads are in .fq format.

Thank you,

Vpi

[mastal]

If you have aligned your reads using an aligner such as bwa or bowtie, then you should have the results in a .sam or .bam file, which IGV should be able to cope with.

[dpryan]

As mastal said, but note that you have to tell IGV to show the bases (right click on an alignment track and select "show all bases").