User: lagartija

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lagartija30
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Posts by lagartija

<prev • 34 results • page 1 of 4 • next >
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Comment: C: How Do I Do Simple Go Term Lookup Given A Gene (Or Mrna) Identifier?
... Thank you for this post ! I can't believe that something so elemental would be so complicated. ...
written 15 hours ago by lagartija30
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Comment: C: How to give merged reads as input in spades
... I think you have an option like --merged but I don't remember. As said you should check the manual and you would propably find it because you can literally give any kind of data to spades. ...
written 17 hours ago by lagartija30
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Functionnal annotation of metagenomes
... Hi everyone, I'm currently starting in metagenomics and I would like to compare the overall functions present in different samples (I already have the sequences of the ORFs). Which method do you recommend for that ? I came across Fun4me that looks like what I am looking for but nobody seems to u ...
protein function metagenomics written 18 hours ago by lagartija30
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Comment: C: GenBank ID to GO term
... I have metagenomic data and I would like to have the GO terms to make a chart of the represented functions in my different samples ...
written 2 days ago by lagartija30
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GenBank ID to GO term
... Hi everyone, I have a blast result from ref seq and I would like to have a quick overview of the functions present in my genomes. Do you know how I can get the GO terms from the NCBI accession number ? I know I can do that with Blast2Go but I am looking for a free alternative. Thank you in adva ...
annotation metagenomics written 2 days ago by lagartija30 • updated 2 days ago by b.nota5.7k
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Comment: C: Annotation of assembled metagenomic data
... Thank you ! I didn't know Kaiju, it seems good. I think this is also possible with QIIME, MetaPhlAn or Clark but I don't know which one to choose. Maybe I should try some of them on a subset of my data to see which one is more suited. ...
written 3 days ago by lagartija30
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Annotation of assembled metagenomic data
... Hi, I have to assign contigs from assembled metagenoms to their taxa and I am looking for a tool that would go faster than a blast. From what I see most of the tools (like Kraken) seem to use the reads for the taxonomic annotation. I don't have access to the reads. Do you know an efficient tool th ...
metagenomics taxonomy written 4 days ago by lagartija30 • updated 4 days ago by Juke-341.7k
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Answer: A: Classify Or Align ?
... Hi, I'm bringing up this discussion again because I have a similar problem and I would like some advice. Working on metagenomics but this time shotgun sequencing, because I cannot use the 16S, I'm wondering if I should use BLAST or a software. I understand that most of the people would agree that ...
written 7 days ago by lagartija30
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Comment: C: use blast+ to blast fine domains in proteins
... Thanks, that was what I was looking for :) ProDOM does have the option to enter a pfam accession number (after trying it I can say that it is way faster than my first method, but it can be complicated to do batch search because the results lacks the query ids. Anyway it is very useful !) ...
written 7 months ago by lagartija30
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Comment: C: use blast+ to blast fine domains in proteins
... I did use hmmer but it doesn't have the option to look through one family domain only. Then I get as result a lot of data I have to go though to analyse for only one function that I am interested in ...
written 7 months ago by lagartija30

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