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NCBI Refseq FTP doesn't have Drosophila sequences.
The problem with Flybase is that there is no single non-redundant database file for the entire transcriptome, but it has individual files for miRNA, ncRNA, miscRNA etc etc.
There is a file called all transctipts but its only mRNA. So I tried combining all these files but there is another problem: Redundancy of sequences. For example the sequence corresponding to the i.d. FBtr0100886 is annotated as mRNA as well as a predicted gene.
Moreover RefSeq ids are not available for all sequences.
Does anyone have a clue where to get the entire Drosophila transcriptome with RefSeq ids
The problem with Flybase is that there is no single non-redundant database file for the entire transcriptome, but it has individual files for miRNA, ncRNA, miscRNA etc etc.
There is a file called all transctipts but its only mRNA. So I tried combining all these files but there is another problem: Redundancy of sequences. For example the sequence corresponding to the i.d. FBtr0100886 is annotated as mRNA as well as a predicted gene.
Moreover RefSeq ids are not available for all sequences.
Does anyone have a clue where to get the entire Drosophila transcriptome with RefSeq ids