Activity for Narendrakumar Chaudhari
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Narendrakumar Chaudhari posted a comment on ticket #9
Dear user, Thanks for using BPGA. If you don't mind, please email the Input_all.seq file to bpgatool@gmail.com rather than publicly. We will post the problem and solution if it is solved.
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Dear User, Look for file gi_name in the bin directory after running BPGA analysis. This file contains gene identifiers with their names (if you use gbk or gbff as input). You can just match the accession numbers in Sequences\REPSEQ_core.txt with gi_name to find their names. Alternatively, if you want the KEGG or COG gene family classification for the same core genome, you can look for K###### numbers or COG#### in Supporting_files\CORE_kegg_hits3.txt or Supporting_files\CORE_COG_hits3.txt, and search...
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Results
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All outputs removed
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You are welcome.
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They are moved to Results folder and other files are moved to sequence folder or Supporting_files folder created inside bin.
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Hello, Rania, The intermediate files are deleted and output is moved to respective folders formed inside bin. However, you can rerun the analsis step 2 directly. If you want to see intermediate files then copy them before exit.
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Hello, Rania, The intermediate files are deleted and output is moved to respective folders formed inside bin. However, you can rerun the analsysi step 2 directly. If you want to see intermediate files then copy them before exit.
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Hello, Rania, The intermediate file are deleted and output is moved to respective folders formed inside bin. However, you can rerun the analsysi step 2 directly. If you want to see intermediate files then copy them before exit.
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Then, close BPGA. Relaunch it and then directly run to step 2.
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Functional Analysis
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Please refer to closed ticket #2 Linux Illegal modulus zero
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Linux Illegal modulus zero
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A few issues on Linux and PC
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For MLST analysis, BPGA will halt and allow the user to make required changes. For MLST analysis, on user defined housekeeping genes Check "mlst_core.txt" for gene details and copy the respective cluster IDs from the first column to "CORE_MLST.txt". CORE_MLST file has core gene family IDs , If you keep only desired IDs phylogeny will run on only those present in CORE_MLST file. You can select by looking at the gene names in mlst_core.txt file. and copy only desired IDs from mlst_core.txt to CORE_MLST...
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Just check from usearch.exe file properties that it is not actually usearch.exe.exe due to hidden file extension. If so remove .exe from file name. Always run bpga from command line or terminal to know more detailed errors. Some systems with Win 10 OS may not allow dll dependaent usearch to run properly. If none of this works re-extract the bpga package from downloaded zip and start over in another location.
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Description of Results
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Interpretation of Results
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Interpretation of Results
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Interpretation of Results
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Interpretation of Results
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Interpretation of Results
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Interpretation of Results
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Interpretation of Results
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Interpretation of Results
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Interpretation of Results
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Interpretation of Results
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Interpretation of Results
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Interpretation of Results
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Interpretation of Results
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Interpretation of Results
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Interpretation of Results
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Interpretation of Results
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Interpretation of Results
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Interpretation of Results
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General Instructions
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Interpretation of Results
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Check if Input_all.seq is not empty. If all are files generated during peparation, relaunch BPGA and start from step 2.
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Check if Input_all.seq is not empty. if all files generated during peparation relaunch BPGA and start from step 2.
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Ben, If you select any fasta option we must ignore your headers because it may not...
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Sorry, @Ben Vezina, We did not get any notification about your post. Check out the...
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