User: lagartija
lagartija • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- Last seen:
- 15 hours ago
- Joined:
- 9 months, 1 week ago
- Email:
- s**********@gmail.com
Posts by lagartija
<prev
• 34 results •
page 1 of 4 •
next >
0
votes
8
answers
27k
views
8
answers
... Thank you for this post ! I can't believe that something so elemental would be so complicated. ...
written 15 hours ago by
lagartija • 30
1
vote
0
answers
45
views
0
answers
... 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
lagartija • 30
0
votes
0
answers
36
views
0
answers
... 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 ...
written 18 hours ago by
lagartija • 30
0
votes
0
answers
68
views
0
answers
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
lagartija • 30
1
vote
0
answers
68
views
0
answers
... 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 ...
0
votes
1
answer
103
views
1
answers
... 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
lagartija • 30
1
vote
1
answer
103
views
1
answer
... 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 ...
0
votes
3
answers
1.9k
views
3
answers
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
lagartija • 30
0
votes
1
answer
152
views
1
answers
... 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
lagartija • 30
0
votes
1
answer
152
views
1
answers
... 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
lagartija • 30
Latest awards to lagartija
No awards yet. Soon to come :-)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1238 users visited in the last hour