User: VS

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VS710
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710
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USA
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3 months ago
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7 years, 10 months ago
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Posts by VS

<prev • 39 results • page 1 of 4 • next >
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Answer: A: When running MITE-hunter, can I split the input genome?
... I have the same question, did you find an answer to this? ...
written 19 months ago by VS710
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Comment: C: Polishing PacBio assembly : The ideal coverage for higly polymorphic species
... Thank you Roxanne for the reply and all the info! I'll write to Mahul. ...
written 2.1 years ago by VS710
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Comment: C: Polishing PacBio assembly : The ideal coverage for higly polymorphic species
... Hi Roxane, I'm facing something similar with the BUSCO stats on my merged assemblies (quickmerge) . In my case, the number of fragmented and missing genes goes significantly higher after the merging step itself. Did you get any insight into what was going on here? Thanks! ...
written 2.1 years ago by VS710
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Comment: C: miniasm GFA format : first field - 'x' and 'a' line
... Yes, The 'a' tag is for the golden path where an entire read is contained within a unitig, while the 'x' tag gives a brief summary of each unitig which can also be inferred from 'S' and 'a' tags. You can check this in the detailed options given in file miniasm/miniasm.1 (where miniasm is your inst ...
written 2.7 years ago by VS710
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Switching from Linuxbrew to Bioconda
... I had been using Linuxbrew as my package manager on an HPC cluster where I do not have root access. Of lately, there seems to be some issue with perl and python env. setup and my jobs on nodes other than the head node keep crashing ex. Illegal instruction error for softwares written in python. Upon ...
hpc linuxbrew bioconda conda written 2.8 years ago by VS710 • updated 2.8 years ago by Devon Ryan92k
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ectools - illegal instruction error
... I'm trying to run ectools to correct PacBio reads (about 1.1Gb) for a small microbial genome. Our cluster has PBS/Torque and no SGE scheduler. So I partitioned the data into 21 directories with ~500 files each. When I run the correct.sh script, it runs and successfully creates cor.fa files in about ...
genome ectools error correction pacbio assembly written 2.8 years ago by VS710
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Comment: C: Removing duplicate reads from Illumina before hybrid de-novo assembly/ before us
... Thanks, this seems reasonable. ...
written 3.3 years ago by VS710
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Removing duplicate reads from Illumina before hybrid de-novo assembly/ before using for correcting PacBio reads or Pac-Bio only assemblies
... Hi All, I was wondering how important is to get rid of exact duplicate Illumina reads before -- 1. Before using it for correcting PacBio reads (planning to use ProovRead) 2. Before using it to polish a Pac-Bio only assembly using Pilon (Assembly was done using uncorrected PacBio reads - miniasm ...
proovread assembly pilon pbcr duplicate reads written 3.3 years ago by VS710 • updated 3.3 years ago by Brian Bushnell16k
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miniasm GFA format : first field - 'x' and 'a' line
... I ran a trial miniasm assembly for my plant genome with about 15x PacBio reads. The output GFA file has some segments (S) and linker(L) lines but also some tags that I could not find documentation for. These were - 'x' and 'a' .. please see example below. Cana anyone point me out a resource with exp ...
miniasm gfa written 3.9 years ago by VS710 • updated 3.9 years ago by Biostar ♦♦ 20
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Quorum error corrector - fastq files as output?
... I am attempting to error correct my illumina short reads using QuoRum error corrector (part of Masurca genome assembler; but I have installed only QuoRum and not Masurca). The output is a fasta file. I am unable to find the option to get the output file in fastQ format instead of fasta. Can anybody ...
software genome masurca sequencing written 4.0 years ago by VS710 • updated 4.0 years ago by h.mon28k

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Popular Question 3 months ago, created a question with more than 1,000 views. For miniasm GFA format : first field - 'x' and 'a' line
Popular Question 11 months ago, created a question with more than 1,000 views. For Postdoctoral Scientist In Plant Computational Genomics
Great Question 2.0 years ago, created a question with more than 5,000 views. For Preferred Tools For Making Analysis Pipeline Flowchart ?
Prophet 2.0 years ago, created a post with more than 20 followers. For Preferred Tools For Making Analysis Pipeline Flowchart ?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Postdoctoral Scientist In Plant Computational Genomics
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For A: Convert Vcf To Hapmap Genotype Format
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Commentator 3.8 years ago, created a comment with at least 3 up-votes. For C: Should We Remove Duplicated Reads In Rna-Seq ?
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: About Human Protein Coding Gene Copy Number Across Genome
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Good Answer 5.7 years ago, created an answer that was upvoted at least 5 times. For A: The Role Of Non-Conserved Regions In Homologous Genes
Popular Question 5.7 years ago, created a question with more than 1,000 views. For Preferred Tools For Making Analysis Pipeline Flowchart ?
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Teacher 5.7 years ago, created an answer with at least 3 up-votes. For A: Insertion Detection Tools
Teacher 5.7 years ago, created an answer with at least 3 up-votes. For A: Convert Vcf To Hapmap Genotype Format

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