User: gb

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gb1.8k
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Posts by gb

<prev • 340 results • page 1 of 34 • next >
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Comment: C: What is an OTU?
... I understand your answer, it is good formulated. But it can be misleading for someone that does not know what a "OTU" is yet. > OTU or Operatinal Taxonomic Unit is used to classify bacteria No, not only bacteria also eukaryotes > An OTU consists of a group of bacteria whose 16S marker gene ...
written 1 day ago by gb1.8k
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Comment: C: QC prior to bacterial genome assembly
... > Nextra Transposase sequences are still there If you are using galaxy you could try trimgalore. This tool already has a parameter specifically for Nextra Transposase ...
written 1 day ago by gb1.8k
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Comment: C: Sequence clustering tool that can break sequences?
... I wanted to reply something similar. I also don't know an existing tool but maybe it helps to look into a method where you re-map the contigs with BWA or minimap and do something with the bam files instead of looking for a clustering method. Maybe you can go trough every position of the bam/sam fi ...
written 25 days ago by gb1.8k
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Comment: C: how to run blastp against nr databse locally
... As far as I can find you need minimum 2.9.0 https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastNews ...
written 4 weeks ago by gb1.8k
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Comment: C: how to run blastp against nr databse locally
... No, you don't have to run makeblastdb. Are you using an old version of blast? You can see that by doing ```blastp -version``` You can either update blast, which is definitely the most recommended thing to do. Or you download the v4 database ftp://ftp.ncbi.nlm.nih.gov/blast/db/v4/ ...
written 4 weeks ago by gb1.8k
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Answer: C: how to run blastp against nr databse locally
... You are missing an alias file, this is a text file that points to all those nr files. See this page for more info https://www.ncbi.nlm.nih.gov/books/NBK279693/ And also instead of ```wget``` you can use ```update_blastdb.pl --passive --decompress nr``` to download the full nr database. The script ...
written 4 weeks ago by gb1.8k
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Comment: C: i can not install uclust
... http://www.drive5.com/downloads/usearch11.0.667_i86linux32.gz ... ...
written 5 weeks ago by gb1.8k
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Comment: C: i can not install uclust
... http://www.drive5.com/usearch/download.html ...
written 7 weeks ago by gb1.8k
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Comment: C: clustalw won't work with macOS catalina suggestions
... Maybe this helps https://support.apple.com/en-us/HT208050 ...
written 7 weeks ago by gb1.8k
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Comment: C: Downloading all COI sequences from BOLD fails
... There are some issues with bold and the API. I remember that at one point you could download all Phylum data except Arthropoda with the API. So you could make a script that downloads the data per Phylum with the API, maybe make a list in python based on this page http://v3.boldsystems.org/index.ph ...
written 8 weeks ago by gb1.8k

Latest awards to gb

Popular Question 8 days ago, created a question with more than 1,000 views. For how to makeblastdb with taxon id's
Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: How much I must feel useless?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: How much I must feel useless?
Appreciated 4 months ago, created a post with more than 5 votes. For A: Removing Duplicates before aligning
Scholar 4 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Scholar 5 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
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
Scholar 5 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
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
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: How much I must feel useless?
Guru 8 months ago, received more than 100 upvotes.
Scholar 8 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Scholar 9 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Supporter 9 months ago, voted at least 25 times.
Scholar 14 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Popular Question 15 months ago, created a question with more than 1,000 views. For how to makeblastdb with taxon id's
Scholar 17 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Scholar 18 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples

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