User: lagartija

gravatar for lagartija
lagartija50
Reputation:
50
Status:
Trusted
Location:
Last seen:
6 days, 3 hours ago
Joined:
11 months, 2 weeks ago
Email:
s**********@gmail.com

Posts by lagartija

<prev • 38 results • page 1 of 4 • next >
0
votes
0
answers
50
views
0
answers
pssm for rpsblast
... Hi, I'm trying to make a database for rpsblast but I don't know how to create a pssm for the database. I have an alignment in fasta format : https://prosite.expasy.org/cgi-bin/aligner?psa=PS50104&format=FASTA and I can also get more information about this domain on prosite : https://prosite.e ...
domains written 12 days ago by lagartija50
0
votes
3
answers
2.1k
views
3
answers
Answer: A: Relative abundance fro metagenomics samples
... Hi, I'm found this post useful because I have the same task (exept that I prefere to work on contigs than on bins). I also mapped the reads to my contigs to get the mean coverage. Is that a sufficient estimation of the (relative) abundance or do I have more steps to do to reduce biases ? ...
written 20 days ago by lagartija50
0
votes
1
answer
133
views
1
answers
Comment: C: running BUSCO on unknown genomes ?
... Thank you for your answer. I think the default parameter is the fruit fly. Can I avoid orfing by augustus somehow ? ...
written 4 weeks ago by lagartija50
1
vote
1
answer
133
views
1
answer
running BUSCO on unknown genomes ?
... Hi, I'm trying to assess my genome completeness and possible contamination with busco. Is it possible to run it several files at the same time ? Is it also possible not to use a reference species when orfing with augustus while running BUSCO ? I am trying to find an equivalent to checkm but for e ...
assembly written 4 weeks ago by lagartija50 • updated 4 weeks ago by Corentin260
0
votes
0
answers
94
views
0
answers
masking low complexity regions in a protein database for BLAST
... Hello everyone, I have a question that might interest people making their own blast protein database. I see there is an option to mask low complexity regions with segmasker before (or after) making a database. How useful is that for protein ? I see why it can really reduce false positives in nucl ...
blast written 7 weeks ago by lagartija50
0
votes
8
answers
27k
views
8
answers
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 9 weeks ago by lagartija50
1
vote
1
answer
256
views
1
answers
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 9 weeks ago by lagartija50
0
votes
0
answers
89
views
0
answers
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 9 weeks ago by lagartija50
0
votes
0
answers
119
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 9 weeks ago by lagartija50
1
vote
0
answers
119
views
0
answers
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 9 weeks ago by lagartija50 • updated 9 weeks ago by b.nota6.4k

Latest awards to lagartija

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1016 users visited in the last hour