User: Paul

gravatar for Paul
Paul40
Reputation:
40
Status:
New User
Location:
India
Last seen:
3 days, 7 hours ago
Joined:
5 years, 9 months ago
Email:
p***************@gmail.com

Posts by Paul

<prev • 34 results • page 1 of 4 • next >
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How to draw a tree from BLAST toolkit output
... Hi I have performed BLAST analysis using command line **blastn -db myDb -query gene.fasta** for which the alignment file is in BLAST format. Is there any way I can take BLAST output to draw a Phylogeny? ...
toolkit tree blast written 16 days ago by Paul40
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Comment: C: How to perform bidirectional BLAST?
... could you send me a tutorial or a link of the software? since I need run it locally ...
written 17 days ago by Paul40
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How to perform bidirectional BLAST?
... I have 100s of complete genome sequences, downloaded from NCBI. And I have query gene sequences which I would like to BLAST against the complete genomes. **To perform the bidirectional BLAST, I would like to create a local database from one genome. The second genome will be queried against the data ...
bidirectional blast written 17 days ago by Paul40
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Comment: C: Genome assembly contig ordering
... If an answer is helpful, upvote it. If the answer resolved your question, mark it as accepted. ...
written 17 days ago by Paul40
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Comment: C: Genome assembly contig ordering
... You can benchmark scaffolding your contigs using various tools, and choose the one with the best output One such tool is: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0951-y However, If the gaps are still high, it could be due to low-coverage sequencing data ...
written 17 days ago by Paul40
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Answer: A: Genome assembly contig ordering
... Use SSPACE. https://academic.oup.com/bioinformatics/article/27/4/578/197626/Scaffolding-pre-assembled-contigs-using-SSPACE https://github.com/nsoranzo/sspace_basic You need to put the contigs in scaffolds. ...
written 17 days ago by Paul40
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Comment: C: how to download all the complete genomes for mycobacteria from NCBI?
... Thanks.. This worked ...
written 24 days ago by Paul40
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how to download all the complete genomes for mycobacteria from NCBI?
... How to download all the complete genomes for mycobacteria from NCBI? I tried downloading the complete genomes from the NCBI site ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/ But couldn't get the exact fasta files with respective mycobacteria. And https://www.ncbi.nlm.nih.gov/genome/?term=my ...
genome ncbi sequence written 25 days ago by Paul40 • updated 25 days ago by 5heikki6.4k
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Comment: C: SPAdes: <jemalloc>: Error in malloc(): out of memory
... Installing the latest version solved the issue... Thanks ...
written 4 weeks ago by Paul40
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Comment: C: SPAdes: <jemalloc>: Error in malloc(): out of memory
... How much more?? around 32 GB RAM? ...
written 5 weeks ago by Paul40

Latest awards to Paul

Supporter 8 weeks ago, voted at least 25 times.
Popular Question 11 months ago, created a question with more than 1,000 views. For Mapping HGNC ID to uniprot ID

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