User: dllopezr
dllopezr • 40
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Posts by dllopezr
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... 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
dllopezr • 40
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... 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
dllopezr • 40
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... 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 ...
written 12 weeks ago by
dllopezr • 40
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... 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 ...
written 3 months ago by
dllopezr • 40
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... 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 ...
written 5 months ago by
dllopezr • 40
• updated
5 months ago by
Fabio Marroni • 2.2k
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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
dllopezr • 40
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... 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 ...
written 6 months ago by
dllopezr • 40
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... 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 ...
written 7 months ago by
dllopezr • 40
2
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1
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... 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. ...
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... 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
dllopezr • 40
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
Popular Question
9 months ago,
created a question with more than 1,000 views.
For Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
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