Tool/Pipeline to get annotations from RNA-Seq
Entering edit mode
3.8 years ago
Heinrich_M • 0

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

RNA-Seq Blast • 655 views
Entering edit mode

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?


Login before adding your answer.

Traffic: 1715 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6