Support for plant genoms
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Zhu xiaobu
Oct 17, 2022, 11:10:56 AM10/17/22
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Hi, JAFFAL developers!
Thanks for making JAFFA available for long sequencing reads, which I believe is very urgent for the identification of fusion transcripts using widely applied long sequening reads. However, fusion genes with long sequencing reads supported has rarely been investigated in plants over animals especially in human. So, I have several questions concerning this.
1, It's noticed that the support of custom genomes has been limited to USCS type as described here. After checking the descriptions, I wonder if JAFFAL could be run on non-UCSC genomes with some modifications, such as adding a prefix "EN" to each genes in the annotaion file?
2, Shall you please provide some suggestions or cautions when applying JAFFAL to plant genomes, such as those caused by difference of repeat content in plants over animals?
Thanks for making JAFFA available for long sequencing reads, which I believe is very urgent for the identification of fusion transcripts using widely applied long sequening reads. However, fusion genes with long sequencing reads supported has rarely been investigated in plants over animals especially in human. So, I have several questions concerning this.
1, It's noticed that the support of custom genomes has been limited to USCS type as described here. After checking the descriptions, I wonder if JAFFAL could be run on non-UCSC genomes with some modifications, such as adding a prefix "EN" to each genes in the annotaion file?
2, Shall you please provide some suggestions or cautions when applying JAFFAL to plant genomes, such as those caused by difference of repeat content in plants over animals?
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