User: russianconcussion

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20
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New User
Location:
United States
Last seen:
1 month ago
Joined:
4 years, 2 months ago
Email:
r****************@gmail.com

PhD candidate in microbiology at Oregon State University.  Wrangling metagenomes, mostly with other people's code (isn't that the definition of hell: other people's code? haha!  Anyhow, thank you if you help me with my own).

Posts by russianconcussion

<prev • 15 results • page 1 of 2 • next >
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Comment: C: "out" parameter for _Fasttree module in Bio.Phylo.Applications from Biopython 1.
... Oops! Yes, you're right; I wrote the command wrong. Regardless, after updating to FastTree 2.1.10, the Biopython wrapper works! It was my ancient version of FastTree that was causing me trouble. Thank you for your help, Rodrigo! ...
written 12 weeks ago by russianconcussion20
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Comment: C: "out" parameter for _Fasttree module in Bio.Phylo.Applications from Biopython 1.
... Hmmm. It definitely doesn't have an '-out' option in my version of FastTree (2.1.3 SSE3). For example, if I try: FastTree -nt -gtr test.codon Works fine and yields a tree in stdout: FastTree Version 2.1.3 SSE3 Alignment: test.codon Nucleotide distances: Jukes-Cantor Joins: balance ...
written 12 weeks ago by russianconcussion20
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Comment: C: "out" parameter for _Fasttree module in Bio.Phylo.Applications from Biopython 1.
... Hi Rodrigo. Actually, my codon alignment is in nucleotides, not amino acids. In a codon alignment, you use a protein alignment to constrain the cognate nucleotide alignment. So I'm sure that the -gtr and -nt options are fine. Here is the head of the codon alignment file: >ID:AMR59844.1 ...
written 12 weeks ago by russianconcussion20
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"out" parameter for _Fasttree module in Bio.Phylo.Applications from Biopython 1.68 doesn't work
... Hi, When I try to run the FastTree wrapper from Bio.Phylo.Applications, it fails, giving me this message: ApplicationError: Non-zero return code 1 from '/home/fetz/genome/phylosift_v1.0.1/bin/FastTree -nt -gtr -out 245_hypothetical_protein.tre 245_hypothetical_protein.codon', message 'Unknown ...
biopython fasttree written 3 months ago by russianconcussion20 • updated 6 weeks ago by Biostar ♦♦ 20
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Comment: C: How to make a custom blast db with taxon IDs from a taxid_map file
... Thanks! Upgrading solved this issue for me too. ...
written 3 months ago by russianconcussion20
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Comment: C: Need help interpreting gdb backtrace from a SAMtools segmentation fault (or help
... Thanks to John Marshall's help with interpreting the samtools segmentation fault, I was able to fix the error. Here is the code that I ended up using to put reads mapped to individual bacterial/phage genes from a multifasta file (a transcriptome bam file from kallisto) onto the bacterial/phage geno ...
written 11 months ago by russianconcussion20
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Comment: C: Need help interpreting gdb backtrace from a SAMtools segmentation default (or he
... Thanks very much, John. I'll start digging into the gdb tutorials, but in the meantime, I'll just try to replicate the steps you took to diagnose the problem and then address that pesky mtid error! (Oh, and I'll update samtools on my laptop. *blush*) ...
written 11 months ago by russianconcussion20
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Need help interpreting gdb backtrace from a SAMtools segmentation fault (or help editing SAM/BAM files!)
... Hi, I'm editing the header, RNAME, POS, and PNEXT of a bam file so that I can transfer read mappings on individual CDS's directly to the complete genome containing those CDS's. To do that, I am using pysam to iterate through a bam file alignment-by-alignment and then building a new alignment to be ...
bam samtools pysam written 11 months ago by russianconcussion20
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How to write FULL genbank files with Biopython SeqIO module?
... Hi, I am trying to split up the Synechococcus genbank files from NCBI Genbank into separate genbank files for each genome.  Some of the genomes have several genbank files because they are draft assemblies.  So, I import the SeqIO library from Bio, parse the conglomerated genbank files, put them int ...
biopython genbank written 22 months ago by russianconcussion20 • updated 21 months ago by Peter5.6k
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Comment: C: Compare multiple samples on KEGG
... Check out the post below.  Not sure if there's anything newer than pathview or not.  I'd aso like to know if there is anything more current. https://www.biostars.org/p/76057/ ...
written 23 months ago by russianconcussion20

Latest awards to russianconcussion

Supporter 11 weeks ago, voted at least 25 times.
Autobiographer 22 months ago, has more than 80 characters in the information field of the user's profile.

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