Tool/Pipeline to get annotations from RNA-Seq
Hello everyone,
I need an automated way to generate and filter annotations of RNA-Seq data. I have a lot of RNA-Seq data to analyze and can't go through BLAST searches individually. I am looking for transposons (reverse transcriptase, ect. ) in repetitive elements in different stages of a parasite. I did a DESeq analysis, but want to classify the transcripts more precisely.
As input I have the RNA-Seq data, but also a BAM with the mapped reads, or the extracted reads in Fasta format. There is also a gff file from the parasite, maybe that can help.
I hope someone can help me. Thanks
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Heinrich_M •
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Some additional information would be useful. What species are you working on? Is there a good quality reference genome and gene annotations already or are you doing this de novo? Do you have a set of transposon sequences already that you are trying to quantify or do you need to characterise these de novo? What did you compare in your DESeq analysis?