Choice Of Insert Size During Alignment

Question

[Honey]

I am working on identification of bacteria/ viruses in infectious material. Have reads of 2X100 bp data. Let us say the bacterial genome size is 10Kb. I am wondering what is the criteria to choose insert size- Should it be as long 0 to 1000bp or it should be small based on read length/ total genome size. Is there a formula/ rule of thumb to follow.

Thanks

Answer 1

[Rahul Sharma]

Hi

You can get this information from the sequencing company, from where you got these sequence reads. Other possibility is to generate rough assemblies using default parameters, And map back these reads onto the rough assemblies. The SAM file having mapped information can be used for mean insert size calculations and insert size SD.

Best wishes, Rahul