Bacterial transcriptome with Rockhopper
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3.4 years ago
Annie • 0

Hello there, I am facing problem in interpreting Rockhopper output. I have bacterial RNAseq data which is single end and 50 bp read length. Reference database is available. There are duplicates for both the samples. I ran Rockhopper using following parameters checked "Reverse complement reads" and "Test for differential expression", but did not get any information regarding fold change. Also I got only Qvalues. I don't know how to find upregulated and downregulated genes from this output. The columns which I got in transcripts.txt are: Transcription_Start, Translation_Start, Translation_Stop, Transcription_Stop, Strand, Name, Synonym, Product, Expression_Control, Expression_Treated, qValue_Control vs Treated.

Any help would be much appreciated!! Thanks and regards!

RNA-Seq Rockhopper Q-value fold-change • 920 views
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Which version are you using?

The last time that I used Rockhopper (2017), I performed de novo transcriptome assembly an differential expression between 2 conditions. I then received 2 output files:

  • summary.txt
  • transcripts.txt

transcripts.txt contained the following columns:

Sequence    Length  Expression M    Expression P    qValue M vs P

Fold-change could be calculated from the 2 'Expression' columns. From the sequence column, I could ran blastx in order to infer the gene / protein relating to the sequence.

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