User: jeetsahu

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jeetsahu0
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Posts by jeetsahu

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How to run SPAdes inside docker?
... Hi, Any running example in cwl script to run SPAdes inside docker? I can run SPAdes without docker but would like to know how to run with docker. ...
container cwl docker written 7 weeks ago by jeetsahu0 • updated 6 weeks ago by Michael R. Crusoe1.1k
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Comment: C: Differences in annotations using Prokka on assembly done by SPAdes
... I used SPAdes for assembly. So what difference in number of base pairs is said to be "acceptable"? How did you arrive at the number of CDS difference? ...
written 10 weeks ago by jeetsahu0
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Differences in annotations using Prokka on assembly done by SPAdes
... I am doing annotation two assemblies, one done by SPAdes and other downloaded from NCBI. I used the data from PRJNA387062 (ncbi). When I used Prokka for annotation on both assemblies, I get large differences between the two annotations. Below is the summary on assembly done by SPAdes. organism: Gen ...
annotation spades prokka written 10 weeks ago by jeetsahu0 • updated 3 days ago by Biostar ♦♦ 20
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Comment: C: SRA: fastq-dump gives different number of sequences
... Thanks, I grepped different symbol. One quick question - Does fastq-dump gives latest dataset used for assembly? if yes how can I get old datasets? ...
written 10 weeks ago by jeetsahu0
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SRA: fastq-dump gives different number of sequences
... I have downloaded read sequences using fastq-dump with split file option and SRR id for paired sequences. But splitted files have different number of sequence reads. As per my understanding, since these are paired-end reads these should have equal number of sequences. $fastq-dump -I --split-files S ...
sra sequence written 10 weeks ago by jeetsahu0 • updated 10 weeks ago by ATpoint12k
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Comment: C: Busco lineage database for Staphylococcus pasteuri assembly
... Thanks for correction. Does prokka also use some model organism for gene prediction ? ...
written 11 weeks ago by jeetsahu0
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Comment: C: Busco lineage database for Staphylococcus pasteuri assembly
... What should be the "model" organism to use in augustus for gene prediction? ...
written 11 weeks ago by jeetsahu0
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Comment: C: Busco lineage database for Staphylococcus pasteuri assembly
... Thanks! will keep this mind. ...
written 11 weeks ago by jeetsahu0
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Busco lineage database for Staphylococcus pasteuri assembly
... I am doing assessment of assembly of Staphylococcus pasteuri genome for the orthologue presence absence using blastn with BUSCO. Which lineage database to use for the same? ...
gene assembly busco genome written 11 weeks ago by jeetsahu0 • updated 11 weeks ago by WouterDeCoster35k
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Comment: C: Sequence reads and complete assembly
... Hahaha... It's still a open question then. You mentioned about a software to compare assemblies. Which software is that? ...
written 11 weeks ago by jeetsahu0

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