User: whatup

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whatup30
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Posts by whatup

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11
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How do I choose among velvet assembled contigs with different k (k-mer) values?
... I have some contigs assembled by velvet using k-mer values ranging from 21 to 31 with step size of 2 (k-mer values: 21, 23, 25, 27, 29, 31).  Oases was also ran on theses assembled contigs since they are for transcriptome assembly. My question is how do I go about picking the best contig out of the ...
velvetg assembly contig velvet written 6.4 years ago by whatup30 • updated 6.4 years ago by Adrian Pelin2.4k
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Comment: C: How to look up GO terms in BioMart using GI ID or Accession ID
... I get many matches from 'gene2accession' database.  However, I get almost no match when I try to match against 'gene2go' database with the extracted gene ID from the 'gene2accession' database.  I noticed that gene2go file size is very small compared to gene2aceesion file which shows that it is missi ...
written 6.4 years ago by whatup30
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Is there a way to run ncbi blastx so that its result will contain GO (gene ontology) terms for each hit?
... I've already tried BLAST2GO and it is either running too slow or unable to connect to its database. So, I was just wondering if there is a way to run blastx in a particular way with some parameter so to add GO (gene ontology) terms for each resulting hits. Maybe there exist a database containing a ...
gene ontology blastx blast go rna-seq written 6.4 years ago by whatup30
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Comment: C: How to run velvetoptimiser on paired-end FASTQ datasets
... yes, it is RNASeq ...
written 6.4 years ago by whatup30
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Comment: C: How to run velvetoptimiser on paired-end FASTQ datasets
... Thank you for your advice!  It's already clearing things up for me.  I'll have a look at Oases as you suggested. ...
written 6.4 years ago by whatup30
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How to run velvetoptimiser on paired-end FASTQ datasets
...   Running Velvet has always been confusing for me.  So, I have always been running it using VelvetOptimiser in order to avoid dealing with searching for optimal parameter values. If I run VelvetOptimiser to assembled a set of paired_end FASTQ sequences, then does this mean I do not need to run Vel ...
assembly velvetoptimiser velvet written 6.4 years ago by whatup30 • updated 6.4 years ago by Philipp Bayer6.9k
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Comment: C: How to look up GO terms in BioMart using GI ID or Accession ID
... I just tried to extract GeneID by matching Accession Number, GI ID, and TaxonID.  Still, there are too many matches and I can't think of any other criteria for matching to narrow it down.  How can I go about choosing one GeneID out of so many? ...
written 6.4 years ago by whatup30
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Comment: C: How to look up GO terms in BioMart using GI ID or Accession ID
... Thank you for taking the time to respond to my post.  I'll give this a try today! ...
written 6.4 years ago by whatup30
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How to look up GO terms in BioMart using GI ID or Accession ID
... Hi, I am working on a research project where I need to add Gene Ontology terms for each hits from NCBI BLAST result.  How can I look up GO terms for each hits using BioMart?  Possible input values that I can use for the GO term lookup are Accession ID, GI ID, and Taxon ID.  I've been attempting to ...
go term biomart gene ontology written 6.4 years ago by whatup30 • updated 4.0 years ago by EagleEye6.7k
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How To Generate A Species Distribution From Blast Xml Output
... Hi, I am very new in bioinformatics field. I have a BLAST XML output file and I need to parse it to generate a species distribution. I was hoping someone could show me how it can be done by Biopython with some examples. thank you, ...
xml biopython blast python written 7.0 years ago by whatup30 • updated 6.4 years ago by Haluk190

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