User: nisrinalulu

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nisrinalulu10
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Posts by nisrinalulu

<prev • 30 results • page 1 of 3 • next >
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Comment: C: Binning of reads vs. binning of contigs in metagenomics
... SO, what is the better between binning reads or binning after contig? ...
written 6 months ago by nisrinalulu10
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Interpret coverage from mapping back de-novo assembly
... Dear all, I have assembly my reads with MEGAHIT to get final contigs. Then I mapping back my contigs with raw reads to get coverage rate with bbmap/bbwrap.sh ref=megahit/IA_result/final.contigs.fa in=raw_data/IA_1.fq in2=raw_data/IA_2.fq out=IA.sam.gz kfilter=22 subfilter=15 maxindel=80 and ...
assembly metagenomic next-gen written 6 months ago by nisrinalulu10
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Comment: C: How to get gene abundance visualization and venn diagram from PROKKA output file
... Dear lieven.streck, Do you have a tutorial or paper to reformatting PROKKA output file to suitable format file for http://bioinformatics.psb.ugent.be/webtools/Venn/? Thank you ...
written 8 months ago by nisrinalulu10
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Comment: C: Venn Diagram for genes
... Dear babarasaki, What type of data input that I can use to produced venn diagram in jvenn? I have file output from PROKKA that I want to visualize in venn diagram. Regards, Lulu ...
written 8 months ago by nisrinalulu10
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Comment: C: How to get gene abundance visualization and venn diagram from PROKKA output file
... I see. Thank you for your reply. I think I can use R packages to produce gene abundance visualization and venn diagram from my data set, but I still looking for the best packages that I can use to produced it. ...
written 8 months ago by nisrinalulu10
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Comment: C: How to get gene abundance visualization and venn diagram from PROKKA output file
... Dear lieven.sterck, Thank you for your reply and your web tool recommendation. The web tool that you mentioned looks easy to use but I have to convert the file format. I want to see gene in venn diagram among 4 my samples. Do you have another software recommendation? Thank you ...
written 8 months ago by nisrinalulu10
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How to get gene abundance visualization and venn diagram from PROKKA output file?
... Hi Everyone, I hope you all doing well. I work with metagenomics data from soil samples and have annotated it using PROKKA. I need visualize PROKKA output to get gene abundance visualization and venn diagram. Do you have a suggestion for me what software or what R packages that I can use to get ge ...
R metagenomics written 8 months ago by nisrinalulu10
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Comment: C: Transforming MEGAN output with Krona
... I didn't do anything after install Krona via conda ...
written 9 months ago by nisrinalulu10
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Comment: C: Error running Prokka
... Dear Bioainata26, I have same problem with you. How do you solved your problem? Do you run script like SMK mentioned? Thank you for your help, Regards, Lulu ...
written 9 months ago by nisrinalulu10
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Comment: C: Qiime file for Krona pie chart?
... Dear Jeremieauger, I also working using Krona but with MEGAN output. I face some problem because my command didn't work in Krona. I wonder what the R package that does Krona chart that you told? Thank you, Regards, Lulu ...
written 9 months ago by nisrinalulu10

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