Francesco Cicconardi

Hi @aganezov, I'm back on CAMSA, and back trying to convert my fasta files into camsa_points. This is the command I'm running. `fasta2camsa_points.py $ASSEMBLY.fasta $ASSEMBLY.LRScaf/scaffolds.fasta EisaPacBio.assembly.v1.0.AllMapScaff.fasta -o $ASSEMBLY.CAMSA.LRScaf` Unfortunately I...

So, I tried with just a bit of the genome and the nucmer step works fine, now delta-filter is running. Six hours and it's still there. Very very slow, and...

Guys, see if this script helps you https://github.com/francicco/-ComparativeGenomicsOfHeliconiini/blob/main/BRAKER-gushrGFF3toBED12v1.0.py F

Great! Happy to help! It took me a while to make it work! If you use it in for a paper let me know! Cheers F

And indeed they are at least two loci But those minus strands are wrong.

Thank you @gpertea, I'm going to try now. F

Didn't improved, actually made it worst, stringtie did not create junctions! The alignment was done using STAR ``` STAR --genomeDir $GENOMEDIR/$SPECIES.STAR.Index $limitBAMsortRAM --twopassMode Basic \ --readFilesIn $RNAR1.fastq $RNAR2.fastq --outFilterType BySJout...

Ok, thanks. I'll give it a look! F

Should I used that mapper? F On Fri, 2 Nov 2018, 14:24 Geo Pertea It's still puzzling that the --fr option did not seem to work properly > there. I'd...

HAHAHAHAH Ok, I'll check HISAT2 too, let's see which perform better! ;) F