shiyi-pan

run new_species.pl error

4

Hi, I want to use this vrey good software to predict genes. But I meet a problem when I train the module. here is my code : $AUGUSTUS/scripts/new_species.pl --species=for_bad_genes_removing --AUGUSTUS_CONFIG_PATH=/ds3512/home/panyp/genome_assess/augustus-3.3.3/config...

No gene can be mapped in enrichGO function

2

Hi, I want to clusterProfiler to do GO enrich analysis. First , I use AnnotationForge to create the Orgdb package because it's non-model specie. It works well. Then I use...

outfile is abnormal

2

hi, I installed the PSMC and tried to run it using the following script: #!/bin/bash # #$ -cwd #$ -j y #$ -S /bin/bash # #$ -l mem_free=4G # PSMC=/ds3512/home/panyp/PSMC/psmc...

Disentangling failed when assemble plant mitochondria genome

2

Hi, I want to use GetOrganelle to assemble plant mitochondria genome and meet a problem. Here is my log file and result files: [assemble_plant_mitochondria.zip](https://github.com/Kinggerm/GetOrganelle/files/7326553/assemble_plant_mitochondria.zip) I have used the mitochondrial genomes...

abnormal eigenvectors

4

Hi, I used find_compartments function to get eigenvectors and compartments, but I think the distribution of eigenvectors is abnormal,here is my eigenvectors: [EigVect1.pdf](https://github.com/3DGenomes/TADbit/files/5824122/EigVect1.pdf) The eigenvalues are negative at both ends...

valid read pairs is too few compared with other tools

4

Hi, I want to use TADbit to detect TADs, the TADbit detect 25,521,413 valid read pairs only ,but other tools such as HiCExplorer could detect 58949201 read pairs using the...

TADs calls problem

3

Hi, I want to detect TADs using this amazing software but I met some problem. here is my code, I just have one experiment from pytadbit import Chromosome from pytadbit.parsers.hic_parser...

gem tbz2 don't has the gem-mappability module

2

Hi, I downloaded the GEM-binaries-Linux-x86_64-core_i3-20121106-022124.tbz2 as you described but when I decompression it ,here is the file in it: gem-2-sam gem-indexer gem-indexer_fasta2meta+cont gem-indexer.man gem-map-2-map.man gem-mapper.man gem-2-sam.man gem-indexer_bwt-dna gem-indexer_generate gem-map-2-map gem-mapper...

error in running the SNPGenie

16

hi, i run the SNPGenie and got warning like that : ## WARNING: The CDS coordinates for gene Glyma.01G115000.3.Wm82.a2.v1.CDS.2 in the gtf file do not yield a set of complete...

hickit.js error

4

Hi, I want to use this tool to find TADs but met a problem. here is my scripts: first, I used minimap2 to mapping HiC reads to my genome: $MINIMAP/minimap2...