User: gb

gravatar for gb
gb590
Reputation:
590
Status:
Trusted
Location:
Last seen:
2 minutes ago
Joined:
1 year, 5 months ago
Email:
m**************@gmail.com

Posts by gb

<prev • 117 results • page 1 of 12 • next >
0
votes
1
answer
63
views
1
answers
Comment: C: FLASh parameters for 250 read length
... No one can answer this question without knowing the length of the fragments. But FLASH gives an very informative output, so you can try different settings and check the changes. As an extra tip, a lot of times it helps to trim of a little of the bad quality ends, it can result in much more merged re ...
written 11 days ago by gb590
0
votes
1
answer
63
views
1
answers
Comment: C: FLASh parameters for 250 read length
... I only use the min-overlap and mismatch ratio. So the reads need to overlap minimal 50 bases and in that overlapping part only allow 10% errors for example. ...
written 11 days ago by gb590
0
votes
0
answers
78
views
0
answers
Comment: C: Remove Duplicates from Illumina AmpliSeq data
... Are it just fasta files? VSEARCH --derep_fulllength ...
written 11 days ago by gb590
0
votes
2
answers
98
views
2
answers
Answer: C: Append number to the fasta sequence header with the times sequence has been repe
... Dont know if you necessarily need to program it yourself but I use `vsearch --derep_fulllength` for this, easy and fast ...
written 18 days ago by gb590
0
votes
2
answers
189
views
2
answers
Answer: A: ncbi database update
... As an addition to the accepted answer you can check the version by running: blastdbcmd -db [yourdatabase] -info If you used and want to use the script `update_blastdb.pl` update_blastdb.pl nt_v5 --blastdb_version 5 --passive ...
written 20 days ago by gb590
0
votes
0
answers
110
views
0
answers
Comment: C: Adding nucleotides to a sequence in a fastq file
... Same as the first comment from Bastien Herve, skip this step. As far as I know you always get your sequences back demultiplexed, only in some rare cases you want to do it yourself. So the pipeline should be able to handle that. I see in de PipeCraft paper that it contains pretty general tools that ...
written 20 days ago by gb590
0
votes
1
answer
89
views
1
answers
Answer: C: Protein sequence with GI number on comment line in FASTA
... You sure about this? You should not use GI numbers anymore https://www.ncbi.nlm.nih.gov/books/NBK431010/#news_03-02-2016-phase-out-of-GI-numbers ...
written 24 days ago by gb590
0
votes
1
answer
130
views
1
answers
Comment: C: Problem when running remote Blast with a big file
... Did this answer helped you, or do you need more information? ...
written 25 days ago by gb590
1
vote
1
answer
130
views
1
answers
Answer: A: Problem when running remote Blast with a big file
... Remote blast is not made for so many sequences at once. There is a certain limit and the ncbi will refuse or close the connection if you exceed it. There is a page somewhere that explains it but can't find it right now. I believe they first slow down your blast and after that they close the connecti ...
written 26 days ago by gb590
1
vote
1
answer
149
views
1
answers
Comment: C: Metagenomics best reference DB
... Genbank also offers a 16S database these days. Dont know how good it is. https://www.ncbi.nlm.nih.gov/refseq/targetedloci/16S_process/ ftp://ftp.ncbi.nlm.nih.gov/blast/db/16SMicrobial.tar.gz ...
written 4 weeks ago by gb590

Latest awards to gb

Scholar 21 days ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Scholar 8 weeks ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Centurion 11 weeks ago, created 100 posts.
Appreciated 4 months ago, created a post with more than 5 votes. For A: Removing Duplicates before aligning
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: How much I must feel useless?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Scholar 6 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Appreciated 7 months ago, created a post with more than 5 votes. For A: Removing Duplicates before aligning
Scholar 7 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Scholar 12 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: 1781 users visited in the last hour