User: nalexandre

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nalexandre10
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Posts by nalexandre

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Plotting time against quantitative variables in R
... Thank you so much! This is perfect. ...
written 14 days ago by nalexandre10
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Plotting time against quantitative variables in R
... Hello, I am running a series of linear regressions between time and some quantitative trait. In order to do so, I need to convert date to some numeric value. I have tried the following: anna$date <- as.POSIXct(anna$date, origin="1861.11.20", format="%Y.%m.%d") But when I try cor.test, I g ...
time-series R ecology written 14 days ago by nalexandre10 • updated 14 days ago by Asaf7.0k
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Comment: C: How do I summarize coverage across many genomes to inform filtering cutoffs?
... Do you mean samtools stats --coverage? I only see this as a subcommand in the new samtools. This is very helpful thank you! ...
written 5 weeks ago by nalexandre10
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How do I summarize coverage across many genomes to inform filtering cutoffs?
... Hello, I used samtools depth to get a textfile of coverage across my genome for ~600 samples. In order to inform coverage cutoffs in the next step I'd like to make a summary/histogram of some sort that summarizes coverage for all of these genomes together. For example, eventually I'd like to say, ...
genome alignment next-gen samtools coverage written 5 weeks ago by nalexandre10 • updated 5 weeks ago by onestop_data160
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Comment: A: Remove and Substitute Fasta Header
... This is great! Thanks so much! ...
written 4 months ago by nalexandre10
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Remove and Substitute Fasta Header
... I have a concatenated fasta file for a series of genbank entries with different headers. I need to edit the fasta headers to all say "BCH" in place of the header up to and including the space after "Archilocus alexandri". For example, DQ432746.1 Archilochus alexandri voucher B02923 cytochrome oxid ...
fasta alignment written 4 months ago by nalexandre10
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Comment: C: EOF Marker absent .bam.pbi files
... Even when I run the command with subreads.bam, subreads.bam.pbi, or subreads.bam.pbi.gz, I get the same errors. How would you suggest preparing raw data for polishing a completed genome? ...
written 8 months ago by nalexandre10
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Comment: C: EOF Marker absent .bam.pbi files
... Yes I do! I am just trying to polish my current genome assembly using arrow. I figured I needed to merge the bam files in order to do this sort of polishing. I was planning to index, align, and sort after merging before running arrow. ...
written 8 months ago by nalexandre10
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Comment: C: EOF Marker absent .bam.pbi files
... I used the gunzip command on all pbi files as the file type was gzip compressed data. ...
written 8 months ago by nalexandre10
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EOF Marker absent .bam.pbi files
... I received a series of subreads.bam.pbi files from my sequencing facility and I unzipped each file. When I try to samtools merge all of the files, I get an error message saying that the EOF marker is absent. I get the following additional message: [E::bgzf_read] Read block operation failed wi ...
assembly sequencing written 8 months ago by nalexandre10 • updated 8 months ago by RamRS25k

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