User: gb

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gb540
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Posts by gb

<prev • 105 results • page 1 of 11 • next >
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Comment: C: Appending strings to fasta header from another file
... I would not put a tab in the header of a fasta file, and I personally use python and a dictionary for this. ...
written 1 day ago by gb540
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Comment: C: Barcode cross contamination
... For me a barcode is a certain marker that is used to identify species like CO1 I don't think that this is what you mean. You should check the quality with fastqc first, I never saw it that the beginning of a read is of bad quality. Also, do you know the sequence of your "barcodes"? If yes you can sp ...
written 1 day ago by gb540
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Answer: A: How to change name of species in FASTA file with BioPython
... Like others also said, we need more info to give the exact answer but I will still give it a try. I assume you have BioPython working, you can use something like this: from Bio import SeqIO with open("input.fa", "rU") as handle, open("output.fa", "a") as output: for record in SeqIO. ...
written 5 days ago by gb540
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Comment: C: Amplicon Sequencing samples identification
... If possible you should ask the lab. You can demultiplex with cutadapt or sabre... Mostly demultiplexing is done during basecalling based on illumina tag. But how many files do you have? In your question you say > 3 x 96 x 2 fastq files So that means you have all the samples right? ...
written 5 days ago by gb540
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Comment: C: Amplicon Sequencing samples identification
... you say that you have a sample sheet in the Plate1 directory, but should you then not also have a samplesheet in the Plate2 and Plate3 directory? ...
written 6 days ago by gb540
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Comment: C: Demultiplex dual indexed reads considering sequence direction
... You could check sabre (https://github.com/najoshi/sabre) and cutadapt (https://cutadapt.readthedocs.io/en/stable/guide.html#demultiplexing). ...
written 16 days ago by gb540
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Comment: C: Standalone Blast tool and command
... I see now you are also asking for the command. It looks like something like this: makeblastdb -in yourprotein.fa -dbtype prot blastx -query yournucseqs.fa -db yourprotein.fa -out output With the command `blastx -help` and `blastx --help` you can see all the options ...
written 19 days ago by gb540
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Comment: C: Standalone Blast tool and command
... Yes, you can do a blastx ...
written 20 days ago by gb540
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Comment: C: SILVA taxonomy ranks
... Looks like the file that I need! Thanks! ...
written 22 days ago by gb540
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Comment: C: SILVA taxonomy ranks
... Here you can find the file for megan but is for the ref_nr99 http://ab.inf.uni-tuebingen.de/data/software/megan6/download/welcome.html. I go check out that file you are mentioning ...
written 22 days ago by gb540

Latest awards to gb

Centurion 19 days ago, created 100 posts.
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Removing Duplicates before aligning
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: How much I must feel useless?
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
Appreciated 5 months ago, created a post with more than 5 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
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Scholar 10 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples

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