Dario Copetti

removing models from a list

2

Hello, I would like to use the GFF3toolkit to remove some gene models (all with one isoform, from an external list) from a gff3 file. I first run `gff3_QC -g...

hinge on a large plant genome

1

Hello, we have ~30x coverage ONT (N50 9.3 kb, 165 Gb) of a ~5 Gb plant genome and we would like to assemble it with HINGE - we wonder if...

out of memory and not producing output

3

Hello, I would like to use racon to error-correct chloroplast (a subset of all reads, made by aligning all reads to the assembly containing cp contigs) PacBio CLR reads and...

Hello, It is the first time I am doing the basecalling on raw ONT data and I would like to run Flappie on the fast5 data. I have a few...

P contigs of length 0

2

Hello, I realized that after Falcon Unzip I have some p-contigs of length 0 (there is an empty line), while there are haplotigs for that sequence. Counting the length: ```...

Nomenclature of FALCON contigs

1

Hi, I am analyzing the p- and a-contigs of a FALCON assembly, and within the p-contigs I see that there are canonical linear contigs (e.g. 003655F), circular contigs (3702) and...

losing lots of haplotigs

2

Hello, I am using this script on an Unzipped assembly (1.3 Gb in total) with default settings (50% of bases to be out). The resulting fasta has many less sequences...

detecting SFSs from short-read unitigs

4

Hello, I wonder if the method to detect SFS strings could be applied to other highly accurate datasets such as unitigs created from Illumina reads (e.g. PE, 2x150 bp, 500...

cannot find input.dat

2

Hello, I would like to run Scaff10x, but after a minute or so that is running, I get this error: ``` [copettid@kp140-95 scaffolding_Rabv2]$ /data/dario/bin/Scaff10X/src/scaff10x -nodes 15 -longread 0 -gap 100...