Inserting N bases at 5' end of clipped reads
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.
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Pierre Lindenbaum
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joshrennick.1 •
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joshrennick.1 •
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out of curiosity, why would you want to do that ?