User: anderson.nb6

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anderson.nb620
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Posts by anderson.nb6

<prev • 6 results • page 1 of 1 • next >
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Which identity to apply when analyzing with BLASTp?
... Hello, I'm using the DIAMOND ([Link][1]) program to align my protein sequences against the CAZY database ([Link][2], also protein). The question is: what identity and p-value should I apply to have a good alignment? I am afraid to put high values ​​and discard results that would be satisfactory. As ...
alignment written 11 months ago by anderson.nb620
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Why are MG-RAST hits higher than submitted sequences?
... Below you can see a sample I sent to MG-RAST. Would you like to understand, why the number of hits obtained is greater than the amount of sequences submitted? **Sample =** s_lhss **Sequences submitted =** 7939561 **Hits obtained =** 8160791 **% Hits =** 116,47% Thank you in advance for your att ...
sequencing next-gen mg-rast written 13 months ago by anderson.nb620 • updated 13 months ago by h.mon24k
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What is the difference between eggNOG, COG and KEGG?
... I can not understand the difference between these databases. Also, when should I use each? Thanks ... ...
genome sequence database next-gen written 16 months ago by anderson.nb620
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Answer: A: How to create heatmap for Genus in Metaphlan2?
... HI Kevin, thanks for the reply. But I had already solved the question. Knowing that it had multiple '.fna', I was able to resolve the issue with the following command sequence: **linux@ubuntu:~$** for f in *.fna; do metaphlan2.py $f --input_type fasta --nproc 4 --tax_lev g > ${f%.fasta.gz}_profi ...
written 17 months ago by anderson.nb620
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How to download KEGG database for metagenomic analysis?
... I have many metagenomic files ".fastq" coming of Illumina sequencing. I would like to analise each file in DIAMOND software (https://ab.inf.uni-tuebingen.de/software/diamond). However, I don't know, where or how I can make the download of the KEGG database. My final aim is to profile the present fu ...
metagenome kegg sequencing written 18 months ago by anderson.nb620 • updated 18 months ago by RamRS21k
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How to create heatmap for Genus in Metaphlan2?
... Hi, I have the following problem: I have in my hands the file 'merged_abundance_table.txt' and I want to create a heatmap of relative abundance for Genus. How should I rearrange the comand below? **linux@ubuntu:~$** grep -E "(s__)|(^ID)" merged_abundance_table.txt | grep -v "t__" | sed 's/^.*s__// ...
genome next-gen metaphlan2 sequencing written 18 months ago by anderson.nb620 • updated 3 months ago by Biostar ♦♦ 20

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