Michał T. Lorenc

training parameters

1

Hi, 1. I have Illummin R1 and R2 of RNA-Seq. Do I need to provide `--stranded`? If yes, how can I find it out? 2. If I ran Trinity on...

Busco Viridiplantae Odb10

3

Hi, How can I add [Busco's Viridiplantae Odb10](https://busco.ezlab.org/frames/plants.htm) to funannotate? Thank you in advance Michal

Hi, I downloaded 1009 proteins for Nicotiana benthamiana from Genbank. After the below filtering I end up with 663 ammino acids sequences: ``` $ grep ">" NbenthamianaGenbankAA.fasta | grep -v...

Hi I installed p5-manager with `sudo pnpm install -g p5-manager` but I got the below error: ``` $ p5 fs.js:646 return binding.open(pathModule._makeLong(path), stringToFlags(flags), mode); ^ Error: EACCES: permission denied, open...

too many genes

1

Hi, I used the following commands for Augustus. However, Augustus predicted 270.000 genes. How is it possible to reduce the count? ``` #bam2augustus bam2hints –intronsonly --in=${r1} --out=${r1}.intron-hints.gff bam2wig $r1 >...

UTRs are missing

6

Hi, I ran HiSat2, MarkDuplicate, removed reads with the lower quality score than 40 and finally only kept properly paired reads. Scallop/StringTie and TransDecoder could predict UTRs but unfortunately, Augustus...

Hi, I used the following commands for Augustus. However, how can I recognise which genes Augustus has predicted as partial or complete? ``` #bam2augustus bam2hints –intronsonly --in=${r1} --out=${r1}.intron-hints.gff bam2wig $r1...

exon-exon-junctions scripts missing

5

Hi, I follow [Incorporating Illumina RNAseq into AUGUSTUS with Tophat](http://bioinf.uni-greifswald.de/bioinf/wiki/pmwiki.php?n=IncorporatingRNAseq.Tophat). Unfortunately, it requires `intron2exex.pl` which has been replaced by [`getIntrons.pl`](https://github.com/Gaius-Augustus/Augustus/commit/47842adb316b4afc6403cce474e1815f479ac2e6). However, Augustus 3.3.3 does not contain the new script. Where...

Container does not to work

5

Hi, I can't access Sequence-server ( http://localhost:4567 ) in the browser after I did the following steps: ``` $ wget -c https://github.com/wurmlab/sequenceserver/archive/refs/tags/2.0.0.tar.gz $ vim docker-compose.yml $ cat docker-compose.yml sequenceserver: build:...

Disable FASTA and FASTA of all hits

7

Hi, Is there a way to disable FASTA and FASTA of all hits to prevent to download the assembly? Thank you in advance, Michal