User: Dave Th

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Dave Th10
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New User
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4 weeks ago
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9 months, 1 week ago
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Posts by Dave Th

<prev • 5 results • page 1 of 1 • next >
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Filter contigs by size: Different output between quast report and python output
... Hi all, I'm trying to filter my contigs dataset into different files by their length such as 500bp, 1kb, 2kb... I'm using below code to produce my output. def contigs_filter_by_length(fasta_input, size, fasta_output): long_contigs = [] #Create an empty list for record in SeqIO.parse(f ...
assembly sequence written 29 days ago by Dave Th10
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SEED Assignment MEGAN6
... Hi all, I would like to use MEGAN for my metagenomics functional analysis. I have downloaded all of the mapping files from MEGAN website and meganized my DAA files. Taxonomy assignment works with all sequences, IP2G assignment also works with more than 75% sequences, but SEED and COG showed almost ...
megan6 seed written 8 months ago by Dave Th10
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Comment: C: MEGAN6 and Daa files from DIAMOND
... I already tried meganizer tool but it said Daa is not Daa file. Yesterday, I found out that the Daa file I got from DIAMOND is not actually DAA file because I used -o output.daa instead of -a output.daa. It's OK now but the number of sequences assigned to SEED is too low. It might because of my sequ ...
written 8 months ago by Dave Th10
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MEGAN6 and Daa files from DIAMOND
... Hi all, I am currently using MEGAN for my soil metagenomics. After using the latest version DIAMOND to get the DAA files, I imported these files to MEGAN along with GI mapping files (GI-Taxo, GI-KEGG, GI-SEED) downloaded from MEGAN6 website. The results show none of my sequences can be assigned to ...
alignment written 8 months ago by Dave Th10
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nr database Diamond
... Hi guys, I want to use DIAMOND for my metagenome Functional analysis. As the instruction, I have to download NCBI nr database (ftp://ftp.ncbi.nlm.nih.gov/blast/db/). Unfortunately, my internet connection is not very stable, so I have to download a multiple nr file nr.**.tar.gz instead of a nr singl ...
alignment protein written 9 months ago by Dave Th10 • updated 9 months ago by h.mon28k

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Popular Question 7 months ago, created a question with more than 1,000 views. For nr database Diamond

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