Hii everyone!
I have received thousands of transcripts generated by a non-stranded RNA-seq and I have just annotated them (I used a in-house bash script to extract from blast results xml the most informative and frequent annotations from blast hits). However, I have found that many transcripts have the same annotation, e.g. two transcripts have been annotated as 1-aminocyclopropane-1-carboxylate oxidase and so on.
Please find attached a file containing some examples of blast alignments of these transcritps. Would you consider these cases as a result of wrong assembly? How can I distinguish assembly error from true splice or isoforms in RNA-seq? Moreover, can I consider two highly similar reverse complement transcripts as only one single transcripts since this is a non-stranded RNA-seq?
Best regards,
Marcio
I have received thousands of transcripts generated by a non-stranded RNA-seq and I have just annotated them (I used a in-house bash script to extract from blast results xml the most informative and frequent annotations from blast hits). However, I have found that many transcripts have the same annotation, e.g. two transcripts have been annotated as 1-aminocyclopropane-1-carboxylate oxidase and so on.
Please find attached a file containing some examples of blast alignments of these transcritps. Would you consider these cases as a result of wrong assembly? How can I distinguish assembly error from true splice or isoforms in RNA-seq? Moreover, can I consider two highly similar reverse complement transcripts as only one single transcripts since this is a non-stranded RNA-seq?
Best regards,
Marcio
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