User: gb

gravatar for gb
gb1.0k
Reputation:
1,020
Status:
Trusted
Location:
Last seen:
13 hours ago
Joined:
2 years, 1 month ago
Email:
m**************@gmail.com

Posts by gb

<prev • 213 results • page 1 of 22 • next >
0
votes
0
answers
67
views
0
answers
Comment: C: Donwload file from within a server
... I think you would call it uploading then instead of downloading. I guess (correct me I am wrong) it would be a similar command but this time "user" and "host" will be the user and host of you own computer executed from the server. ``` scp path/to/file/tomove user@host:path/to/file/topaste ``` In pr ...
written 4 days ago by gb1.0k
1
vote
0
answers
106
views
0
answers
Comment: C: DADA2/R Programmer Needed for One-Time Job
... I know this is a job tread but still want to share that in my experience if you can not identify on species level it has much more to do with the sample itself and the used reference then the actual pipeline. Edit: to test your pipeline for the species identification part you can also just blast a ...
written 4 days ago by gb1.0k
0
votes
1
answer
112
views
1
answers
Comment: C: NGS data analysis training
... The OP added his specific needs after my post, maybe it can still be usefull. I will add the disclaimer. Thanks ...
written 5 days ago by gb1.0k
0
votes
1
answer
149
views
1
answers
Comment: C: How to solve the different number of hits from tblastn when I use the option -pa
... oh! thanks for updating your post ...
written 5 days ago by gb1.0k
0
votes
1
answer
68
views
1
answers
Comment: C: Fast all to all global alignment
... USEARCH: https://drive5.com/usearch/manual/cmd_allpairs_global.html VSEARCH: https://github.com/torognes/vsearch Sorry, wrote this comment before but removed it unintentionally ...
written 11 days ago by gb1.0k
0
votes
0
answers
119
views
0
answers
Comment: C: how many genomes from BLAST hit should be considered for phylogeny tree analysis
... Ah, thanks for the heads up. Indeed, especially with phages and the replication rate. Would it be an option for the OP the find some genes that are present in all the genomes so more then only one terminase and paste them together as one sequence and use that to make an alignment? ...
written 11 days ago by gb1.0k
0
votes
0
answers
119
views
0
answers
Comment: C: how many genomes from BLAST hit should be considered for phylogeny tree analysis
... > Also, that is not the concern for me at the moment. Yes it is, otherwise the tree is useless. If the genomes are from the same organism you could do it based on the snps in the exons or orf's. But that requires some work. For evolutionary distance using marker genes like 16S, COI, ITS etc. is ...
written 11 days ago by gb1.0k
0
votes
0
answers
119
views
0
answers
Comment: C: how many genomes from BLAST hit should be considered for phylogeny tree analysis
... What if one of the genomes is assembled poorly, will that not influence the tree? ...
written 12 days ago by gb1.0k
0
votes
1
answer
96
views
1
answers
Comment: C: Biopythons PairwiseAligner, ".aligned" attribute doesn't work.
... Not deprecated(?): From the cookbook (16 July 2019) applied on your code: from Bio import Align aligner = Align.PairwiseAligner() my_target = "ACTTGATCTTTCGT" my_query = "CTTGATCT" aligner.gap_score = -1 aligner.match = 1 aligner.mismatch = -1 aligner.quer ...
written 12 days ago by gb1.0k
2
votes
1
answer
154
views
1
answers
Answer: A: Query cover in global alignment
... A global alignment does not give a coverage. "It will always try a coverage of 100%", a global alignment will try to align the **full** sequence in the best possible way. ...
written 12 days ago by gb1.0k

Latest awards to gb

Guru 12 days ago, received more than 100 upvotes.
Scholar 12 days ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Scholar 13 days ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Supporter 18 days ago, voted at least 25 times.
Scholar 5 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Popular Question 6 months ago, created a question with more than 1,000 views. For how to makeblastdb with taxon id's
Scholar 8 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Scholar 10 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Centurion 10 months ago, created 100 posts.
Appreciated 12 months ago, created a post with more than 5 votes. For A: Removing Duplicates before aligning
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: How much I must feel useless?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Scholar 14 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Appreciated 15 months ago, created a post with more than 5 votes. For A: Removing Duplicates before aligning
Scholar 15 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Scholar 20 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1803 users visited in the last hour