Hi,
I am trying to identify small peptides of the male accessory glands in a de novo transcriptome assembly of med fly.
I have 100bp paired end Illumina data of male and female sex organs. The idea is to combine the data to do the assembly, map back the reads and look at transcripts expressed specifically in males. With this subset I could try to BLAST against known sex peptides of other species, although, they are not well conserved.
The problem is the size of these peptides. Most of them are only 30-40 amino acids long. With the Illumina reads being already 200 bp long it is possible that every read that is not integrated into a longer transcript will pop up at this length. It is likely that the peptides are in the noise of the assembly.
I wonder if anyone had to deal with a similar problem in the past and could give me a few hints on how to do such an analysis with very small transcripts.
I don't want this first post to become too long to read, however, if it is of interest I can give details on how the assembly and mapping is done in a follow up.
Thank you!
I am trying to identify small peptides of the male accessory glands in a de novo transcriptome assembly of med fly.
I have 100bp paired end Illumina data of male and female sex organs. The idea is to combine the data to do the assembly, map back the reads and look at transcripts expressed specifically in males. With this subset I could try to BLAST against known sex peptides of other species, although, they are not well conserved.
The problem is the size of these peptides. Most of them are only 30-40 amino acids long. With the Illumina reads being already 200 bp long it is possible that every read that is not integrated into a longer transcript will pop up at this length. It is likely that the peptides are in the noise of the assembly.
I wonder if anyone had to deal with a similar problem in the past and could give me a few hints on how to do such an analysis with very small transcripts.
I don't want this first post to become too long to read, however, if it is of interest I can give details on how the assembly and mapping is done in a follow up.
Thank you!
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