User: bitpir

gravatar for bitpir
bitpir60
Reputation:
60
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New User
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2 hours ago
Joined:
1 year, 8 months ago
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r*******@gmail.com

Posts by bitpir

<prev • 21 results • page 1 of 3 • next >
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Answer: A: how to plot multi pheatmap into one figure
... Hi all, I know my answer is ~3years too late but I just want to put it out there and hopefully people will find this useful in the future. I found the answer [here][1] Basically, user hrbrmstr mentioned that "The manual page for pheatmap() clearly states in the Values section that it returns a list ...
written 7 weeks ago by bitpir60
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Answer: A: do blast search using gi numbers
... Hi all, Thank you for the responses. Somehow I am able to use GI numbers as queries for rpsblast using ncbi-blast-2.6.0. This was also tested by Dr. Wayne Matten from NCBI User Services.Here's what I did: 1. Sort and output only unique GI numbers, else a C++ exception error will occur (see htt ...
written 5 months ago by bitpir60 • updated 5 months ago by genomax40k
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Answer: A: ncbi error C++ exception
... Thank you for your responses! I think I figured out the error. This happens when there's duplicate queries in the file (1400_to_4999_combined_protein_id_ac, which contains gi numbers). If I sort and output the unique gi numbers, the C++ error went away. The error "Protein BLAST database 'Pfam nr' do ...
written 5 months ago by bitpir60
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ncbi error C++ exception
... Hi there, I encounter this problem when I tried to run rpsblast: /ncbi-blast-2.6.0+/bin/rpsblast -query /data/1400_to_4999_combined_protein_id_ac -db Pfam -out /data/rpsout Warning: [rpsblast] Error initializing remote BLAST database data loader: Protein BLAST database 'Pfam nr' does not ...
ncbi blast written 5 months ago by bitpir60
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Comment: C: do blast search using gi numbers
... Hi h.mon, I'm using rpsblast+ from blast+ package 2.5.0 and 2.6.0(latest). Yes, I suppose downloading fasta files will be the quickest solution, although my queries are rather large (>700K). NCBI's CD-search accept gi/accession number as query (https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb ...
written 6 months ago by bitpir60
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Comment: C: do blast search using gi numbers
... Thank you for your response! Unfortunately, I didn't see any improvement when I converted my query from gi number to accession (eg EFL06024.1). The error regarding "Protein BLAST database 'Cog/Cog nr' does not exist in the NCBI servers" still there.... ...
written 6 months ago by bitpir60
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do blast search using gi numbers
... Hi, I'm trying to do an rpsblast using ncbi-blast-2.5.0+. I have a file containing gi numbers as my query and my command line is below. rpsblast -query t -db results/Cog/Cog -out rps-blast.out -evalue 1e-2 -outfmt 6 Oddly the rpbslast keeps giving me this error: Warning: [rpsblast] Error ...
blast written 6 months ago by bitpir60
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finding NCBI protein ID and associated COG ID
... Hi there, I am new to the metagenomic field. I recently did a blastx of my contigs using the nr database. With the results, I plan to categorize the protein hits with COG_ID and COG functions. I am using the cog2003-2014.csv database that's available from the NCBI website, by looking up the protein ...
nr database blastx cog written 6 months ago by bitpir60
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Comment: C: customize reference genome
... Perfect, just what I need. Thanks! ...
written 6 months ago by bitpir60
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customize reference genome
... How do you customize a reference genome, say, hg19, and make into a personalized reference genome in fasta format? I don't have the phased sequence information, but I have the fastq's, bam, and vcf formats. ...
dna-seq written 6 months ago by bitpir60 • updated 6 months ago by WouterDeCoster25k

Latest awards to bitpir

Teacher 18 days ago, created an answer with at least 3 up-votes. For A: how to plot multi pheatmap into one figure
Scholar 5 months ago, created an answer that has been accepted. For A: do blast search using gi numbers
Popular Question 11 months ago, created a question with more than 1,000 views. For samtools counting unique mapped reads

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