User: gb

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gb1.5k
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Posts by gb

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Comment: C: BLAST database index file
... You can download it here ftp://ftp.ncbi.nlm.nih.gov/blast/db/ pre-formatted. You can also use the ```update_blastdb.pl``` tool. ...
written 3 days ago by gb1.5k
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Comment: C: How to get 1 top hit only for each query in blastx
... Can it be ```max_hsps```? https://www.ncbi.nlm.nih.gov/books/NBK279684/ ...
written 5 days ago by gb1.5k
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Answer: A: Exclamation mark in Samtools mpileup output
... Try to add ```-Bx``` to your command. Short story long: mpileup is originally made to call variants. To not count the overlapping bases between the forward and reverse reads twice samtools changes the quality score to "!". This "!" has a phred score of 0 and will be ignored in the variant calling ...
written 7 days ago by gb1.5k
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Comment: C: Vegetable databases usage
... https://www.biostars.org/p/420614/#420684 ...
written 12 days ago by gb1.5k
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Comment: C: No bcl2fastq found on path
... I guess you need to install bcl2fastq... https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software/downloads.html ...
written 13 days ago by gb1.5k
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Comment: C: Collapsing BAM based on seq and positions
... Is this not what mark duplicates from picard does? http://seqanswers.com/forums/showthread.php?t=7776 https://www.biostars.org/p/3917/ https://www.biostars.org/p/309887/ https://broadinstitute.github.io/picard/ There are many more post about this but then you may know what to look for and if ...
written 14 days ago by gb1.5k
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Comment: A: blastx local terminal
... You could download taxonomic information here: ftp://ftp.ncbi.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.zip To get the taxids you can filter the rankedlineage file. EDIT: Changed the link ...
written 18 days ago by gb1.5k
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Answer: A: Family level taxonomic annotation
... https://github.com/feargalr/Demovir ...
written 19 days ago by gb1.5k
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Comment: C: Megahit assembly after merging files with PEAR
... DADA also has a merging step, so if you use the one from DADA or use PEAR it does not matter I think. ...
written 19 days ago by gb1.5k
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Comment: C: Megahit assembly after merging files with PEAR
... Although I very much agree that this is the answer to the original question I want to add something just for the OP to continue his/hers research. Call it metabarcoding instead of metagenomics (Like the name you don't have genomes) Also take a look at the unoise algorithm (implemented in VSEARCH an ...
written 19 days ago by gb1.5k

Latest awards to gb

Appreciated 7 days ago, created a post with more than 5 votes. For A: Removing Duplicates before aligning
Scholar 7 days ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Scholar 25 days ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Scholar 27 days ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Scholar 4 weeks ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Scholar 5 weeks ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: How much I must feel useless?
Guru 4 months ago, received more than 100 upvotes.
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 4 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Supporter 4 months ago, voted at least 25 times.
Scholar 10 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Popular Question 11 months ago, created a question with more than 1,000 views. For how to makeblastdb with taxon id's
Scholar 13 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Scholar 14 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Centurion 15 months ago, created 100 posts.
Appreciated 16 months ago, created a post with more than 5 votes. For A: Removing Duplicates before aligning
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning

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