FeGenie

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error depth = open("%s/%s.depth" % (outDirectory, cell)) | HELP PLS.

1

Hi Arkadiy, I am trying to run FeGenie with various bam file aligning to 2 different genomes. The command I am using is: FeGenie.py -bin_dir final_megahit_co_assemblies/ -bin_ext fa -out fegenie_total_A_C_output...

DrRumble

About iron-sulfur proteins

1

Hi,thanks for your good jobs. I want to identify the iron-sulfur proteins of MAGs. I see that you will update this function in the near future. When will it be...

maocheng2020

Use of ORFs

2

Hi, Thank you for your tool. I am currently using FeGenie on contigs and have tried to use it on ORFs as well. My results are quite different and those...

STabuteau

where was the data for protein DmkA obtained from？

1

Hi, Thank you for your tool. We would like to ask where the data for protein DmkA was obtained from. We didn't find the protein sequence of DmkA in NR...

xdli009

'Namespace' object has no attribute 'hbm'

1

Hi Arkadiy, I am trying to use FeGenie to identify proteins involved in iron reduction. My inputs are two amino acid fasta files from two metatranscritptome data. they are significant...

Sxxnwei

Error in hclust(d = dist(x = fegenie.scaled))

1

Error in hclust(d = dist(x = fegenie.scaled)) : NA/NaN/Inf in foreign function call (arg 10) Calls: as.dendrogram -> hclust Execution halted

manik-123

Renamed contigs?

4

Hi Arkadiy, Thank you for all that you do! I am noticing that FeGenie renumbers/names contigs within individual MAGs' depth files. For those of us who cross-reference output from different...

JBuongio

geneSummary file

3

Hi Arkadiy, Just a quick question -- are the outputs in the geneSummary files showing **all** encoded HMM hits and their ORFs or are these hits that are both encoded...

JBuongio

Error - ValueError: could not convert string to float: 'EMPTY'

38

Hi there, I am aiming to make plots with coverage data for several bam files. I get .depth files and .csv files (as well as ORF_calls and HMM_results. However, there...

JBuongio

Permission denied when moving files

6

Hi Arkadiy, thanks very much for developing this great tool :) I'm trying to implement FeGenie, however, near the end of the analysis this error is raised: `Pre-processing of final...

aidanfoo96