User: ksipes

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ksipes0
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Posts by ksipes

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Mapping Gene Annotations to COG Classifications
... I have a list of gene names that I got from [Prokka][1] annotations. I want to know the [COG Categories][2] of each of the annotated genes. I have a list of about 15,000 so a way to batch script this would be the best. I'm thankful for any suggestions. [1]: https://github.com/tseemann/prokka ...
gene annotation cog prokka kegg written 29 days ago by ksipes0 • updated 29 days ago by Mensur Dlakic2.5k
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Comment: C: How to view read mapping from Bowtie2, Samtools, etc
... That previous command shows the reference sequence name (NODE_###_##...) and then all of the contig mapped numbers. How does adding up the reads mapped to each sequece show me the percent of reads from each bin when I don't know what contigs from each fastq went into which bin ? ...
written 6 weeks ago by ksipes0
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Comment: C: How to view read mapping from Bowtie2, Samtools, etc
... How do I figure out the percent of reads that went into each of the bins that mapped to ? In the beginning, I concatenated my .fa files for my index file to mapp against all of my paired fastq files. Now i just want to know the number of reads from the fastq files make up each one of the bins. ...
written 6 weeks ago by ksipes0
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How to view read mapping from Bowtie2, Samtools, etc
... I am wanting to be able to view the percentage of reads from metagenomic bins to the paired fastq files. I have already completed making .bam files, and .sam files and sorted, and indexed the sam files with samtools. I just need the percent of reads from my bins that are found in any of the seven ...
bowtie2 samtools bowtie readmapping written 6 weeks ago by ksipes0 • updated 6 weeks ago by Asaf6.5k

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