Christophe Klopp comments

Results 30 comments of


                                            Christophe Klopp

Homozygous diploid trio assembly assigning largely ambiguous nodes to only one haplotype

Hi, Thank you for hifiasm, great tool! I'm having a similar problem with a bovine genome assembly in which 200Mb are missing from haplotype 1 and the dot plot with...

using local RNA-Seq files

Hereunder is the content of my metadata file BioProject,SRA Accession,Tissues,Description,Date,Read Length (bp),Ended,RNA Seq,process,Location DUMMY,local,test,cDNA;Illumina HiSeq 3000,3/15/17,202,PE,1,1, local_1.fastq and local_2.fastq files are in the root directory were I launch finder.

using local RNA-Seq files

I've modified the location but this has no impact on the results 2021-03-04 14:38:14,036 - finder - INFO - Started processing data for test 2021-03-04 14:38:14,037 - finder - INFO...

using local RNA-Seq files

Here is the link to the progress log file : http://genoweb.toulouse.inra.fr/~klopp/tmp/progress.log

using local RNA-Seq files

We have updated the code but the error is still there. How can I find the commands which finder runs? Here is the complete progress.log 2021-03-04 18:50:03,563 - finder -...

using local RNA-Seq files

Here it is : BioProject,SRA Accession,Tissues,Description,Date,Read Length (bp),Ended,RNA Seq,process,Location DUMMY,/work/klopp/Project_VenomGene.1468/Finder/RNA-Seq2,test,cDNA;Illumina HiSeq 3000,3/15/17,202,PE,1,1,

using local RNA-Seq files

Thank you. Finder ran until braker but stopped due to lack of memory. Is there a table giving the memory, cpu requirements and processing time per genome size?

using RNA-Seq gzipped fastq files

Thank you but I find your solution suboptimal. First becauce STAR is able to align fastq.gz, files, second because of the used disk space and third because we usually use...

STAR CPU limit

Sorry, I did not get which commands you want me to execute.

Question about preparing FASTA Input Files for Assessing Haplotype-Resolved Genomes of Autotetraploid Species Using Merqury

Hi, One way to produce qv and completeness for polyploid is to produce the values two by two for haplotype couples and then merge all the haplotypes and produce the...