User: mdgn

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mdgn10
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Posts by mdgn

<prev • 11 results • page 1 of 2 • next >
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Comment: C: NameError: global name '...' is not defined
... Usage: python transdecoder_wrapper.py transcripts num_cores strand(stranded or non-stranded) output_dir This is the `--help` output. To be honest the pipeline is outdated despite of an update on the scripts. The softwares have compatibility issues with outdated versions and so on. I thought givi ...
written 10 days ago by mdgn10
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Comment: C: NameError: global name '...' is not defined
... The output should contain pep and cds files for downstream analyses with some descriptive outputs as well. @Joe, I will look into this, from my search it might be a problem about Biopython. @h.mon, Yes I used it before, but since I was following this pipeline this time I tried to stick with it. ...
written 10 days ago by mdgn10
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NameError: global name '...' is not defined
... Hello, I am trying to use a script for the software Transdecoder. But I am getting this error. I created a new conda environment with all necessary prerequisites. $ python transdecoder_wrapper.py Trinity_lactea.largest_cluster_transcripts.fa 2 stranded ./ TransDecoder.LongOrfs -t /home/papa ...
software error gene rna-seq python written 10 days ago by mdgn10
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How to extract chloroplast genes from exon capture data using reference chloroplast genome
... Hello everyone, I have Megahit assemblies of 5 closely related plant species from targeted sequence capture (exons). What I want to do is, using a previously assembled reference chloroplast genome to extract the cp genes (exons) from these 5 assemblies to use them in maternal phylogeny. Sadly, my s ...
chloroplast genome gene assembly written 3 months ago by mdgn10
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Comment: C: Testing Illumina reads for contamination
... I have WGS so DNAseqs. ...
written 4 months ago by mdgn10
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Comment: C: Testing Illumina reads for contamination
... I understand. I am working with plants and I don't know if I can follow a similar way regarding databases. ...
written 4 months ago by mdgn10
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Comment: C: Testing Illumina reads for contamination
... Yeah initially I did that. Thank you though. ...
written 4 months ago by mdgn10
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Comment: C: Testing Illumina reads for contamination
... There was an image embeding option so I used it. Is it better now? ...
written 4 months ago by mdgn10
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Testing Illumina reads for contamination
... Hello everyone, I am trying to figure out if there is a contamination in my Illumina reads which have bimodal GC content per sequence. I quality filtered to have enough reads with a decent length with optimal quality. Only problem is my bimodal GC content. ![enter image description here][1] Is i ...
genome sequencing written 4 months ago by mdgn10 • updated 4 months ago by RamRS24k
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Comment: C: How to identify Substitution rate is per time unit in baseml
... Thank you for the offer but I used the older version and I got the sub. rate today. There might be a bug I don't know, another colleague tried his previous (worked) files with the newest version and he had the same problem. Thanks though. ...
written 5 months ago by mdgn10

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