question about perl

[houyong]

I am a new comer in this field.recently,i have to finish a bioinformatics task.the contents are as follow:
basic data(from IIlumina GA II or GA IIx):
1.long pair reads form sequencing:1.fq and 2.fq;
2.the scaffold constructed by the reads;
task:
after the process of sequencing a long pair fragment,using perl to assess the distribution of the length of mate-pair inserts,and find out how many sequences can be assembled at last.
Can somebody explain what the task want me to do?As a beginer,I really don't know what the length of mate-pair inserts mean?and How to identify the sequences can be used to assembled.
Thanks very much!

[simonandrews]

With Illumina paired end sequencing you produce two short (normally somewhere between 36-100bp) sequence tags which come from either end of an original sequence fragment in your library, and which sit on opposing strands.

The length of inserts in your library can vary but would normally be between 100-500bp. I guess therefore that the question you're being asked is to figure out what the actual distribution of fragment sizes in the original library was.

Normally you'd do this by mapping the reads back against a known reference sequence and seeing how far apart they mapped. In your case you say you have a scaffold constructed by the reads which suggest you've assembled them. You could use this assembly to see how far apart the sequence pairs assembled. For this to work though you'd have needed to have assembled your sequences already. I can't think of any way of figuring out the insert size distribution from just a set of fastq files without using a reference or building an assembly.

[houyong]

thanks very much

With Illumina paired end sequencing you produce two short (normally somewhere between 36-100bp) sequence tags which come from either end of an original sequence fragment in your library, and which sit on opposing strands.

The length of inserts in your library can vary but would normally be between 100-500bp. I guess therefore that the question you're being asked is to figure out what the actual distribution of fragment sizes in the original library was.

Normally you'd do this by mapping the reads back against a known reference sequence and seeing how far apart they mapped. In your case you say you have a scaffold constructed by the reads which suggest you've assembled them. You could use this assembly to see how far apart the sequence pairs assembled. For this to work though you'd have needed to have assembled your sequences already. I can't think of any way of figuring out the insert size distribution from just a set of fastq files without using a reference or building an assembly.

thank you very much! I've got it.Just aligne the 1.fq and 2.fq to the reference sequence(the assembled scaffold).then calculate the distance between the two pair-reads.and about the second question,may i have to align the reads each other to remove the dupicated one?