Inserting N bases at 5' end of clipped reads

Question

[joshrennick.1]

I have been dealing with some clipping of sequencing reads such that the reads align nearly identically, but some reads are trimmed at the 5' end. I want to be able to insert Ns at bases that are missing alignment at the start, what is the best way to do this?

    Seq 1: ATGCTAG
    Seq 2: TGCTAG
    Seq 3: GCTAG

Becomes:

    Seq 1: ATGCTAG
    Seq 2: NTGCTAG
    Seq 3: NNGCTAG

During processing, I have been using Samtools / Bowtie2 / cutadapt and several R libraries, so a solution using one of them would be ideal but open to other suggestions.

[Pierre Lindenbaum]

out of curiosity, why would you want to do that ?