more contigs of different samples to a gene fragment

Question

[xiaofungwu]

When analysing transcrptomics or metagenomics of two or more samples, there may be many contigs similar with each other. How can I regard those contigs as a same gene fragment? which index or parameter can be employed? Is there any high effective analysis tool to compare expression level of two or more metatranscriptomic samples?

Thanks for everyone noticing this question and replying, I will appreciate them.

[smilefreak]

You could use last to generate these results quickly, using some threshold to determine whether you have the same gene fragment.

Answer 1

[Prakki Rama]

For the question "How can I regard those contigs as a same gene fragment? which index or parameter can be employed?"

may be you can blast your contigs to reference and see which contigs are hitting to the same gene from both conditions. They must be from the same gene.