User: arsilan324

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arsilan32480
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Posts by arsilan324

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How to generate OTU table including fasta sequences from QIIME output?
... Hi all, I need some help in making OTU table (excel format) which includes read abundance, taxonomy, and fasta sequences. I used QIIME to generate output and it gives me two separate files. I have tried a few methods to combine both files but it's not working for me. I am wondering if you can guide ...
fasta mothur miseq otu table qiime written 7 months ago by arsilan32480 • updated 7 months ago by andres.firrincieli480
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Comment: C: Sorting taxonomy table
... Yes, it has multiple values of same taxon in each column. So first of all i want to combine (sum) them to make a single value and then arrange them. ...
written 13 months ago by arsilan32480
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Sorting taxonomy table
... Hi all, I am trying to sort OTU table with assigned taxonomy; it looks like this (only four rows are shown below), Treatment_A Value_A Treatment_B Value_B Treatment_C Value_C Sulfuritalea 1492 Sulfuritalea 1273 Sulfuritalea 3770 Sideroxydans 6480 Sulfuritalea 683 Sulfur ...
otu_table R next-gen written 13 months ago by arsilan32480
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High Resolution KEGG pathway
... Hi all, I have finished KEGG mapping for my genome. Now I want to download one KEGG pathway but with high resolution or at least bigger font size. Can you please tell me how can I do that. Here is the link to pathway. https://www.kegg.jp/kegg-bin/show_pathway?@ko04626/reference%3dwhite/default%3d% ...
images kegg rna-seq written 14 months ago by arsilan32480
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Comment: C: counting number of genes located on positive or negative strands
... Thank you to both of you! It worked.. Thanks!!! ...
written 17 months ago by arsilan32480
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counting number of genes located on positive or negative strands
... Hi all, Maybe this is a very basic question but I must tell that I am not a bioinformatics person. I just need to count total number of positive and negative genes located on chromosome in .genes or .gff3 file. Can you please comment how can I do that? Thanks in advance ...
gff3 htseq written 17 months ago by arsilan32480 • updated 17 months ago by mike-zx190
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(Closed) Merging cells in each rows using semicolon?
... Hi all, This may be a very basic question but I am not able to fo since last hour. I want to merge cells in each row using a comma or semicolon. The data looks like OTU_1 23 15 273 51 127 190 220 83 k__Bacteria p__Chloroflexi c__SJA-15 o__C10_SB1A f__C10_SB1A g__Candidatus Amarilinum s__ The ...
R statistics excel data written 20 months ago by arsilan32480
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Answer: A: How to fix Error in `$<-.data.frame`(`*tmp*`, "Kingdom", value = character(0)) :
... The new version ampvis2 worked perfectly. Thanks! ...
written 20 months ago by arsilan32480
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Comment: C: How to fix Error in `$<-.data.frame`(`*tmp*`, "Kingdom", value = character(0)) :
... Apologies. Here is the command. amp_rabund(data = dsn, tax.aggregate = "Genus", tax.add = "Phylum", scale.seq = 100) ...
written 20 months ago by arsilan32480
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How to fix Error in `$<-.data.frame`(`*tmp*`, "Kingdom", value = character(0)) : replacement has 0 rows, data has 2407
... Hi all, I am stuck with this error. Error in `$<-.data.frame`(`*tmp*`, "Kingdom", value = character(0)) : replacement has 0 rows, data has 2407 This is what I get after running this command amp_rabund(data = physeqP, tax.aggregate = "Genus", tax.ad ...
rank abundance phyloseq written 20 months ago by arsilan32480

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Popular Question 13 months ago, created a question with more than 1,000 views. For how to extract/grep lines containing specific word?
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