User: hjafar

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hjafar10
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4 months ago
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1 year, 2 months ago
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h*****@kacst.edu.sa

Posts by hjafar

<prev • 7 results • page 1 of 1 • next >
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Divine tool configuration file requirments
... I have install the Divine tool (https://github.com/hwanglab/divine/blob/master/documents/tutorial/divine_tutorial.md) but when I run the following command, I have got the error as shown below. $ divine.py -v ./Pfeiffer.vcf -o ./Pfeiffer.noHpo IOError: check [beta_fit = /home/genomic-lab/Documents/k ...
software error next-gen written 5 months ago by hjafar10
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Comment: C: Prokka bacteria genome annotation
... Hi Agata, Kindly send me the running command line of filtering contigs with blastnn? ...
written 12 months ago by hjafar10
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Issue wiht pseudogenes in bacteria genome
... I have submitted bacteria genome to NCBI and I have received a pseudogenes issue in bacteria genome as shown following : Before we can assign your accession number, there are a few issues that require your attention. We have annotated your genome and found that the number of pseudogenes is greate ...
genome written 13 months ago by hjafar10 • updated 12 months ago by Biostar ♦♦ 20
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Comment: A: Trimming sequences based on NCBI contamination screen report
... I received the following feedback from NCBI as shown below. Can you tell me your suggestions ? Thank you for your GenBank submission. SUBID BioProject BioSample Localid Accession Organism ----------------------------------------------------------------- ...
written 14 months ago by hjafar10 • updated 14 months ago by genomax85k
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Comment: C: Trimming sequences based on NCBI contamination screen report
... Yes, I am trying to submit plain fasta data through the genome submission to NCBI. I submitted the genome using the following tree step yesterday and I am waiting for the feedback. #Trim adapters bbduk.sh in=~/r.fasta out=trimmed.fasta ktrim=r k=23 mink=11 hdist=1 ref=/bbmap/resources/ada ...
written 14 months ago by hjafar10 • updated 14 months ago by genomax85k
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Comment: A: convert bam to fasta
... Use the following command line of samtools: ## Converting BAM to fastq/fasta ## samtools fasta input.bam > output.fasta samtools fastq input.bam > output.fastq ...
written 14 months ago by hjafar10 • updated 14 months ago by genomax85k
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Comment: A: Trimming sequences based on NCBI contamination screen report
... Can you tell me how to solve this feedback from NCBI as shown below? I have trimmed adapters and removed contaminants and then mapped/splited fasta file as flowing command line . #Trim adapters bbduk.sh in=~/r.fa out=trimmed.fa ktrim=r k=23 mink=11 hdist=1 ref=/bbmap/resources/adapters.fa ...
written 14 months ago by hjafar10 • updated 14 months ago by genomax85k

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