SolayMane

Long read triming

1

I have a question about internal timing of masurca. Does masurca trim adaptors from long read sequencing data set (ONT/PacBio)?

I want to calculate nucleotide diversity using vcftools based on vcf output as bellow without success: vcftools --vcf snps.vcf --window-pi 1000 --window-pi-step 200 --out pi-out the out pt is empty...

Extract the genes with variants

2

I have a question not an issue about Snippy. Could we extract the genes that are affected by snp/indels from the query genomes?

I would like to add here a part about using Edirect to retrieve data =from NCBI repositories, scripts will be provided to query nuccore, assembly, gene.. databases.

SNPgenie for one bacterial strain

1

Dear Chase, I have a vcf file for snps of one strain against a ref. Can I use SNPgenie to calculate Pi trough the whole genome using sliding window? Sincerely

Fuannotate comapre Aborted

3

**Are you using the latest release?** Running 1.8.15 **Describe the bug** A clear and concise description of what the bug is. **What command did you issue?** funannotate compare -i GCA_000149955.2_ASM14995v2_genomic/annotate_results/Fusarium_oxysporum_f._sp._lycopersici_4287_4287.gbk...

funannotate annotate gb2parts()

7

**Are you using the latest release?** Yes **Describe the bug* I run funanotate annotate with the updated version on funannotate gbk file **What command did you issue?** funannotate annotate --genbank...

I have aligned my genome to the reference one using blastn ( with e value 0.00001 ). Chromosomer mapped the fragments fo the query on several chromosome. I found that...

regex pattern do not match

2

I runt the fellowing command : ````bash python general_read_density_data.py TE_input/Cleaned_Fusarium_oxysporum_f.sp._albedinis_Foa_44.tsv out_TE_density/ "FOA_(.*?).h5" ```` I got this error : ````bash The strings of chromosomes in your unprocessed hdf5 files: ['Chr_1', 'Chr_10',...

can't find compleasm_to_hints.py

1

I run BRAKER3 with the following command ````bash # BRAKER CALL: /software/BRAKER/scripts/braker.pl --threads 40 --useexisting --genome=/ArganiaGenomics/Assembly_Colora/results/assemblies/yahs_primary.fa.masked --sp ecies=Argania_spinosa --rnaseq_sets_ids=S1,S2,S3,S4,S5,S6 --rnaseq_sets_dir=/ArganiaGenomics/Transcriptomics/ --busco_lineage=embryophyta_odb12 --COMPLEASM_PATH=/sof tware/compleasm_kit --GENEMARK_PATH=/software/GeneMark-ETP --TSEBRA_PATH=/software/TSEBRA/bin ````` I got this error...