User: dllopezr

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dllopezr40
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Posts by dllopezr

<prev • 36 results • page 1 of 4 • next >
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Answer: A: Blast script over multiple databases
... I already do it Because my databases have this name structure: `T"x"P"x"_T"x"` when x is a 1 to 4 number I create all the strings and passed it in the blast command #!/bin/bash for T in `seq 1 4`; do for P in `seq 1 4`; do for t in ...
written 12 weeks ago by dllopezr40
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Comment: C: Blast script over multiple databases
... Hi Lieven When I say "aliases" I refer to the name of the blast database is not a file but a name that represents the files. Example: The makeblastdb produces 3 files with names: T1P1T0.nhr, T1P1T0.nsq and T1P1T0.nal, but the name of the blast database to pass to blastn script is only T1P1T0 with ...
written 12 weeks ago by dllopezr40
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Blast script over multiple databases
... Hi community I have a folder with multiple blast databases. I want to run blastn over all databases and produce one output for each database. I'm trying something like that for i in `find . -name 'name_of_database'`; do time blastn -db "$i" -query Sondas_100.fasta -out "$i".out -ou ...
multipledatabases script blastn written 12 weeks ago by dllopezr40
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BLAST filter by identity percentage and query cover
... Hi community! For the purpose of my work I need that the blast ouput don't show me the hits with 100% identity and 100% query coverage with the command -perc_identity 100 I obtain only the hits with 100% identity, but I want the opposite. I've try something like -perc_identity <100 but seems B ...
query cover identity percentage blast written 3 months ago by dllopezr40
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sorting columns by same values to do DEG analysis
... Hi community! I am working with metagenomic output from MG-RAST, but the columns don't match and I need to solve this before doing my DeSEQ analysis. The table is something like this GeneName Count GeneName Count GeneName Count GeneName Count GeneA x GeneB x GeneA x Ge ...
sorting columns differential expression written 5 months ago by dllopezr40 • updated 5 months ago by Fabio Marroni2.2k
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Comment: C: Mock Metagenome Gene Content
... Thanks for your Answer Nitin. The problem is that I don't want to find out the abundance of an organism, I want to count the abundance of some genes of interest. For example, how many time the gene "nifH" is present in the sample, for this purpose I need to know the organism that carry this gene, ho ...
written 6 months ago by dllopezr40
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Mock Metagenome Gene Content
... Hi, community! I need to work with a mock metagenome community for the optimization of the alignment parameters of a tool I've found this community: https://www.nature.com/articles/sdata201681, that is composed of 26 bacterial and archaeal genomes. For the purpose of my work I need to know the a ...
metagenome mock community gene content written 6 months ago by dllopezr40
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Filter by Tax Rank in Kegg API
... Hi, community! I am using the KEGG REST API to retrieve plain text files of some genes of interest. For example: `http://rest.kegg.jp/get/enzyme:1.18.6.1` to obtain all info of the enzyme 1.18.6.1, including the genes associated with, or `http://rest.kegg.jp/find/genes/nifh` to obtain a list o ...
rest api taxonomy kegg written 7 months ago by dllopezr40
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Cutadapt wrong behaviour
... Hi, community! I am using cutadapt v 1.18 in paired end mode to trim shotgun metagenomic sequences. My command line is the following: cutadapt -q 20,20 -m 70:70 -a "ADAPTER_FORWARD" -A "ADAPTER REVERSE" -o forwardoutput.fastq -p reverseoutput.fastq input_forward.fastq input_reverse.fastq -e 0. ...
cutadapt written 7 months ago by dllopezr40 • updated 7 months ago by gb780
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Comment: C: Change python version to run cutadapt
... Hi Kevin! I Tried the @finswimmer solution but a "permission" message appear. Tomorrow I will talk to my system administrator and I will try again. I will keep you notified. Regards! ...
written 7 months ago by dllopezr40

Latest awards to dllopezr

Popular Question 12 weeks ago, created a question with more than 1,000 views. For How to include complete labels names in R boxplot
Scholar 12 weeks ago, created an answer that has been accepted. For A: Blast script over multiple databases

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