Mathavan Muthaiyan

Hello I am trying to download the database using the command (metawrap_prokka) [suresh@node4 2.Clean]$ kraken-build --standard --threads 50 --db standard Error Message: Found jellyfish v1.1.12 --2021-12-20 10:44:08-- ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz => ‘nucl_gb.accession2taxid.gz’...

How to remove the isoform in the trasncript.fa file?

3

Hello , I am doing the denvo transcriptome assembly, please guide me how to remove the isoforms in the transcript.fa file, The output of transcript.fa file has transcript start as...

What is hg19_ref_all.txt file?

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Hi The annotate step need this file hg19_ref_all.txt, I want to know is that file representing the human GTF file? or how I can generate the file (hg19_ref_all.txt)

Hi there I have some doubts about the assembly results; could you please assist me? I created a genome assembly of a plant genome with a genomic size of ~120-200...

Gene Prediction Challenges and Strategies for Phytophthora meadii

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Hi there, I am currently working on gene prediction for the pseudo-fungus _Phytophthora meadii_. Unfortunately, I couldn't locate any relevant gene models associated with this species. Is it possible to...

Gene Prediction Workflow : Utilizing BREAKER3 and Generating Protein Files from GTF Output

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I am presently engaged in studying the genome of Dalbergia, commonly known as Indian rosewood. Regrettably, I currently lack RNA-Seq data or protein files pertinent to this genome. Nonetheless, I...

hi, I am trying to download the kraken database using this command kraken-build --standard --threads 24 --db standard but I got an error, can you please help me Error Message...

Hello, I have created quant files, while executing the Rapclust --config config.yaml, I got the error mentioned below home/nucleome/.local/bin/RapClust:26: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader...

DCC throws value error?

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hi, I have executed the DCC, the circular RNA counts and co-ordinates files are generated. For finding the CircSkipJunction I got the error mentioned below. Can you please guide me...

duplicate reads in the count matrix with difference expression value?

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Hi, I have done the circular RNA prediction, the files CircCoordinates,CircRNACount,CircSkipJunctions and LinearCount generated. The CircRNACount file has duplicate rowname with different expression values. Can you please guide me on...