Francesco Cicconardi

Wrong orientation with Linkage Map

7

Dear @tanghaibao, I'm experiencing problems using AllMaps with LM. In some instances, the scaffolding with the LM with AllMaps generates wrong orientation, resulting in artifacts in the inversion. Here I'll...

Hi, I'm trying to train Augustus for UTRs. I got this as a final result. It looks like the UTR failed. ``` ******* Evaluation of gene prediction ******* ---------------------------------------------\ |...

Hi, I wanted to use my dataset to train augustus for UTRs, I think I have to generate the `myspecies_utr_probs.pbl` file. Where can I find a tutorial for doing that?...

Hi, I'm trying to compile `bam2hint` & `bam2wig`, I can't. For `bam2hint` this is the Makefile: ``` BAMTOOLS = /newhome/tk19812/software/bamtools INCLUDES = -L$(BAMTOOLS)/include/src LIBS = $(BAMTOOLS)/lib/libbamtools.so -lz SOURCES = bam2hints.cc...

SPAdes + RaGOO

3

Hi, I'm setting un a pipeline to assemble short-read data at low coverage using a reference assembly of a very closely related species (GS: ~400Mb). Without going into details I...

Interpreting BUSTED-PHenotype analysis

2

Hi, I'm exploring the BUSTED-PHenotype analysis. This is the result of it. I didn't quite understand the results. ``` ### Obtaining branch lengths and nucleotide substitution biases under the nucleotide...

esource: invalid source key: RM

11

Hi, I'm many genomes to annotate with BRAKER only few fail. The error I get from one of the is in the `Third etraining - now with CRF` step. Etraining...

GUSHR output

2

Hi, I'm using GUSHR to get the UTRs with `--AUGUSTUS_ab_initio --gff3 --addUTR=on`. I guess the final output would be `augustus.hints_utr.gtf`/`augustus.hints_utr.gff3`. Unfortunately, both don't have the `exon` feature. That makes the...

--UTR=on works?

18

Hi, I was wondering if the UTR prediction now works, because the pipeline stopped during that stage, `utrs.gff` is empty. Thanks F

ValueError: Number of processes must be at least 1

6

Hi, I'm having this type of error, not always. I don't understand the reason why. Any help? ``` (folding) [tk19812@bp1-login01 Eueides_Etal.Etal0000684G814b.5]$ python -u -W ignore /user/work/tk19812/software/RoseTTAFold-1.1.0/DAN-msa/pick_final_models.div.py pdb-3track model 28 Traceback...