FASTA-format file using terminal command line

Question

[12sp]

using two files which are a subset of paired-end reads from a eukaryotic transcriptome (read length 90, insert size 200 I am trying to create a FASTA-format file containing all assembled transcripts 300 bp or larger. Each FASTA record should include a unique gene id (any alphanumeric identifier, e.g. gene 1234).

[Joe]

Ok. But what's your question and what does your data look like?

[GenoMax]

Since you have not clarified this I will ask.

1. Are these RNAseq data?
2. Are you trying to assemble those reads into a de novo fasta format transcriptome?
3. Have you looked into what is involved in going from raw data to assembled sequence?
4. If this is eukaryotic data then one possible place to start is Trinity page: https://github.com/trinityrnaseq/trinityrnaseq/wiki

[GenoMax]

Now this is sounding like an assignment based on the edits you made. If it is you should clearly state that. At this point you have a starting point with trinity. You now will need to show some effort on your part to get further assistance.