N character in Illumina fastq format

[balamudiam]

Hi everyone,

I downloaded Illumina data from NCBI short read sequencing archive. I used script located http://maq.sourceforge.net/fq_all2std.pl to conver the data to fasta format. The converted fasta data is having N character including regular DNA characters like A,C,G and T.

My assembler runs only with A,C,G and T. Is the conversion correct? Is there any additional script to be run to get rid of N character.

Thanks
Bala

[simonandrews]

You can certainly get N in sequences from the Illumina pipeline. If your assembler can't handle those then you'll either need to trim your sequences at the first N, convert all Ns to an arbitrary normal base, or just discard the sequences which contain Ns. I don't know if there are scripts out there already which will do this, but any of those options should be pretty easy to implement.