Hi.

I know that what soft-clipped reads are.

But when facing sam files, also, there are many hard clipped reads.

and I cannnot figure out what differences between them even though I check the sam specification.

Could you explain the difference of them?

I attached the easily understood figure

![< image not found >][1]

 [1]: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723002/figure/F1/
soft-clipped: bases in 5' and 3' of the read are NOT part of the alignment.

hard-clipped: bases in 5' and 3' of the read are NOT part of the alignment AND those bases have been removed from the read sequence in the BAM file. The 'real' sequence length would be length(SEQ)+ count-of-hard-clipped-bases