User: shibl_a

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shibl_a20
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Posts by shibl_a

<prev • 15 results • page 1 of 2 • next >
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Taxonomy from Pfam database
... I have a fasta file with >1000 sequences as a result of an hmmsearch against the pfam database. I would like to extract the lineage information (i.e. from phylum to genus or species) of each of those sequences and place it in the header (maybe instead of the current header). For example; Currentl ...
bioinformatics taxonomy pfam written 5 months ago by shibl_a20
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Kaiju or MetaPhlAn2?
... A question for those who have experience with metagenomic datasets...which of those two tools would you prefer to use with a metagenomic dataset derived from a seawater sample in terms of reliability and more accurate representation of the taxa..?? Thanks! ...
kaiju taxonomy metaphlan2 metagenomics written 16 months ago by shibl_a20
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Normalization to fit bars on GraPhlAn generated cladogram
... Hello, I recently generated a cladogram on GraPhlAn from my Metaphlan2 output and wanted to add a ring displaying the relative abundances of each clade. I created a text file with this information according to the example (https://bitbucket.org/nsegata/graphlan/src/default/examples/guide/annot_3.tx ...
normalization graphlan metaphlan2 cladogram written 16 months ago by shibl_a20 • updated 13 months ago by francesco.asnicar0
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HUMANn2 test error
... Installed humann2 recently on Ubuntu 16.04 Ran `humann2_test` and all was ok Ran `humann2_test --run-functional-tests-tools` and all was ok Ran `humann2_test --run-functional-tests-end-to-end` and got the following one error (below are the last few output lines of this command ...
humann2 functional analysis testing error written 17 months ago by shibl_a20 • updated 17 months ago by WouterDeCoster43k
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Comment: C: CheckM and pplacer error
... That was the first thing I tried but this is what the conda command returns Solving environment: failed PackagesNotFoundError: The following packages are not available from current channels: - pplacer Current channels: - https://conda.anaconda.org/biocond ...
written 18 months ago by shibl_a20
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CheckM and pplacer error
... I installed checkm using bioconda and downloaded pplacer from its site. I then moved all the pplacer executables into the checkm bin. When I run this command: $ checkm lineage_wf --pplacer_threads 2 checkm_input checkm_output I get this output: ****************************************** ...
genome quality phylogeny bins checkm pplacer written 18 months ago by shibl_a20
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Answer: A: REALPHY and JAVA compatibility issue or not?
... Resolved (for now)...the problem was in the config.txt file ...
written 19 months ago by shibl_a20
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REALPHY and JAVA compatibility issue or not?
... I'm trying to use REALPHY to generate a phylogeny tree based on whole (bacterial) genomes. When I run the commands "REALPHY_V112 realphy_input realphy_output" or "java -jar RealPhy_v112.jar ~/Desktop/realphy_input ~/Desktop/realphy_output" I get the same error: Exception in thread "main" java.lang. ...
whole genome-based phylogeny java tree realphy written 19 months ago by shibl_a20
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Comment: C: Organizing tools/ software
... I like the idea of being able to have everything I need for a project in one place. I'll check out docker. Thanks for the inspiration. ...
written 20 months ago by shibl_a20
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Comment: C: Organizing tools/ software
... Thank you for your suggestion. It was the closest I could find to describe my question. If there were other tags I would've used them. ...
written 20 months ago by shibl_a20

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Popular Question 4 months ago, created a question with more than 1,000 views. For hmmscan using Pfam-A.hmm target database

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