CWang_ecoevo
CWang_ecoevo
Hi, Is this problem solved? I am using v2.1.6, and use RNAseq as evidence to braker, but only get 47.2% of the BUSCOs. My genome gets 98.8% of the BUSCOs...
And I run protein evidence plus RNA evidence and the BUSCO did not get significant higher, from 47.2% to 51.3%.... Any suggestions here? thanks, Cui
Hi again, Just to let you know my problem solved. It wasn't about the version of braker2, but the amount of RNAseq data. I obtained braker results as above when...
Hi, I run it with haploid mode for 8 rounds of correction and didn't get the final.hic file either? Intreastingly, I soft linked the merged_nodups.txt file from the juicer output...
thanks Olga. I somehow managed to finish the pipeline in another run, and the result looks quite satisfying! best, Cui
Hi, Thank you for the information. Does it run if I have diamond in the PaTH? Yes I run it like that. The help menu runs fine, and then it...
> Hi Lars, This script skip some transcripts, such as: HiC_scaffold_19 AUGUSTUS start_codon 5934653 5934655 . + 0 transcript_id "file_1_file_1_jg143570.t1"; gene_id "file_1_file_1_jg143570"; do you know what could be the reason?...
Hi Lars, I sent you the file from email. The braker.gtf file was obtained by running braker2 with both RNAseq and prothint evidences. Please let me know how it goes...
Thanks Lars. That worked! Cui
Hi, did anyone test using gffread to improve annotation? How is the result? thanks, Cui