User: gauravdube007

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Posts by gauravdube007

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Comment: C: GeneMark-ES exits with "error, file not found: info/training.fna"
... Update: After posting, I have used the same command on another assembly which has better genome statistics than the previous one and it worked !!! It seems the problem is with 'probuild', as it requires atleast 10Mb of good data for training (ref: [https://www.researchgate.net/post/Genemark-ES_error ...
written 11 days ago by gauravdube0070
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Comment: C: GeneMark-ES exits with "error, file not found: info/training.fna"
... Hi Santosh, I don't have training.fna in the 'info' directory. The following files are present in the info/ directory: training.trace, dna.trace, dna.multi_fasta, dna.general, dna.gc.csv, dna.gap_distr. Please find my update below. ...
written 11 days ago by gauravdube0070
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Comment: C: Genemark-Es Gtf Output Conversion To Mod
... Hi angelshiza, Recently, I have encountered with the same error ("error, file not found info/training.fna"). Have you found a solution to troubleshoot this error ? Any help is appreciated. Thanks in advance. ...
written 11 days ago by gauravdube0070
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GeneMark-ES exits with "error, file not found: info/training.fna"
... Dear All, I am trying to use GeneMark-ES Suite 4.32 to predict genes from a fungal genome. But GeneMark exits with: > error, file not found: info/training.fna To run the program, I am using the following command: ./gmes_petap.pl --ES --fungus --sequence CBS_contigs.fasta.masked The log fi ...
software error gene prediction genemark written 11 days ago by gauravdube0070
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Comment: C: How to generate a scale for a phylogenetic tree?
... Thanks Dan for your reply. Please kindly take a look at this image generated by FigTree. I have generated this tree with 1000 bootstrap support using Seqboot-> Neighbor -> Consensus workflow of PHYLIP v3.69 with default parameters. Image Link:  The scale you see in this image has a value as ...
written 20 months ago by gauravdube0070
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Comment: C: Non-ATGC, small-case, 'N' characters in Fastq file
... Thanks a lot Brian. ...
written 22 months ago by gauravdube0070
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Non-ATGC, small-case, 'N' characters in Fastq file
... Hi All, I am currently performing genome assembly. I have generated the consensus fastq file using the commands below. But the fastq file consists of lot non-ATGC characters (highlighted with bold). What are these characters and how to handle these?  Commands used to generate Fastq file: >>b ...
fastq genome-assembly non-atgc small-case written 22 months ago by gauravdube0070 • updated 22 months ago by Brian Bushnell13k
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How to generate a scale for a phylogenetic tree?
... Dear All, I have generated phylogenetic trees for a gene dataset by Neighbor joining and Maximum likelihood methods with 1000 boostrap replicates using PHYLIP v3.69 package. I observed in various research articles that the phylogentic trees also have a scale-bar (which mostly represents residue sub ...
nj scale bar phylogenetic tree ml written 22 months ago by gauravdube0070 • updated 22 months ago by Dan Gaston6.8k
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Comment: C: How To Visualize The Quality Of Sequencing Data In Colorspace (Solid) Format?
... Hello Leandro Lima can you please help me with this post ?? Can Anyone Suggest Me A Program For Converting Dot-Bracket Notation Format To Standard Hybridization Format. Thanks in advance. ...
written 3.2 years ago by gauravdube0070
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Comment: C: Download data from OMIM
... Hello Biojl can you please help me with this post ?? Can Anyone Suggest Me A Program For Converting Dot-Bracket Notation Format To Standard Hybridization Format. Thanks in advance. ...
written 3.2 years ago by gauravdube0070

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Popular Question 15 months ago, created a question with more than 1,000 views. For How to generate a scale for a phylogenetic tree?

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