User: Prakki Rama

gravatar for Prakki Rama
Prakki Rama2.2k
Reputation:
2,200
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Location:
Singapore
Website:
https://asearchforsolu...
Twitter:
Prakki_Rama
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Google Scholar Page
Last seen:
2 days, 14 hours ago
Joined:
6 years, 10 months ago
Email:
r***********@gmail.com

Bioinformatics Research Associate 

Linkedin: http://tiny.cc/fn92qy

Posts by Prakki Rama

<prev • 410 results • page 1 of 41 • next >
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Comment: C: Error using in Smalt aligner program
... It is a bug that is fixed in 0.7.6 version. From the SMALT release history: > - fixed bug in 'smalt map -p' resulting in the "assertion failed" error message. This could occur when a read aligned across two successive sequences in the reference file for which the index was > constructed, ...
written 26 days ago by Prakki Rama2.2k
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Comment: C: Tool for calculating sequence statistic values (e.g. N50) for multiple bins
... Hi Brian, Just a comment. I used the wrapper you mentioned above. I get the output as following: Main genome scaffold N/L50: 3/804334 Main genome contig N/L50: 3/804334 It appears N and L values should be other way around : `N/L50: 804334/3` ...
written 26 days ago by Prakki Rama2.2k
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Comment: C: Missing sequences in local NT database
... Actually, this is not straight forward. Downloading large files is timing out. So, for now, I just used NCBI eutils to download my sequence from NCBI online: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=sequences&id=NC_019090.1&rettype=fasta&retmode=text This also ...
written 7 weeks ago by Prakki Rama2.2k
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Comment: C: Missing sequences in local NT database
... @gb These are [merged data entries][1] in NCBI databases. [1]: http://asearchforsolutions.blogspot.com/2018/02/merged-entries-in-non-redundant.html ...
written 9 weeks ago by Prakki Rama2.2k
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Comment: C: Missing sequences in local NT database
... Sure Thanks much @lieven !! I will try it and post again! ...
written 9 weeks ago by Prakki Rama2.2k
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Comment: C: Missing sequences in local NT database
... I am trying to download fasta file from FTP. But, connection is timed out. I also tried downloading using axel from terminal. Still had the same problem. Any other ideas to access the fasta sequence data? ...
written 9 weeks ago by Prakki Rama2.2k
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Comment: C: Missing sequences in local NT database
... I assumed they are same. ...
written 9 weeks ago by Prakki Rama2.2k
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Comment: C: Missing sequences in local NT database
... Thanks for posting NCBI's reply @lieven.sterck. Let me check the accession in the fasta file then. ...
written 9 weeks ago by Prakki Rama2.2k
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Missing sequences in local NT database
... Hi all, I have downloaded the whole NT database locally for running BLAST. During my search, I miss some sequences in the local NT database but are found from NCBI website. These are some of the accessions which could not be found in local NT: Error: [blastdbcmd] Entry not found: NC_019090.1 ...
ncbi nt blast blastdbcmd written 9 weeks ago by Prakki Rama2.2k • updated 9 weeks ago by lieven.sterck3.3k
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Comment: C: How To Retrieve Genbank Records With Range Of Accession Numbers
... Thanks for the command. It was very helpful!! ...
written 11 weeks ago by Prakki Rama2.2k

Latest awards to Prakki Rama

Great Question 3 months ago, created a question with more than 5,000 views. For Meaning of Chromatin state
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: [Noob Doubt] Mapping and Annotation.
Popular Question 10 months ago, created a question with more than 1,000 views. For How to generate AGP format using contigs and scaffolds
Popular Question 10 months ago, created a question with more than 1,000 views. For How to generate AGP format using contigs and scaffolds
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: [Noob Doubt] Mapping and Annotation.
Popular Question 13 months ago, created a question with more than 1,000 views. For How to generate AGP format using contigs and scaffolds
Epic Question 14 months ago, created a question with more than 10,000 views. For Aligning Reads To A Reference Transcriptome
Popular Question 16 months ago, created a question with more than 1,000 views. For How to generate AGP format using contigs and scaffolds
Librarian 19 months ago, created a post with more than 10 bookmarks. For Assessing The Quality Of De Novo Assembled Data
Appreciated 19 months ago, created a post with more than 5 votes. For A: Assessing The Quality Of De Novo Assembled Data
Epic Question 19 months ago, created a question with more than 10,000 views. For Assessing The Quality Of De Novo Assembled Data
Student 19 months ago, asked a question with at least 3 up-votes. For Assessing The Quality Of De Novo Assembled Data
Popular Question 20 months ago, created a question with more than 1,000 views. For Meaning of Chromatin state
Popular Question 20 months ago, created a question with more than 1,000 views. For Which peak is homozygous and heterozygous in Kmer plot for Genome estimation
Popular Question 21 months ago, created a question with more than 1,000 views. For #Reads Per Contig Information From Assemblies Other Than Velvet
Commentator 21 months ago, created a comment with at least 3 up-votes. For C: samtools idxstats on indexed BAM failed
Great Question 21 months ago, created a question with more than 5,000 views. For Minimum Or Optimal Rpkm Value To Find If A Transcript Is Significant
Prophet 2.2 years ago, created a post with more than 20 followers. For Assessing The Quality Of De Novo Assembled Data
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Quickest way to extract subset of reads from huge fastq file
Scholar 2.4 years ago, created an answer that has been accepted. For A: RNAseq: remove contaminants before or after mapping reads?
Appreciated 2.4 years ago, created a post with more than 5 votes. For Assessing The Quality Of De Novo Assembled Data
Librarian 2.4 years ago, created a post with more than 10 bookmarks. For Assessing The Quality Of De Novo Assembled Data
Epic Question 2.4 years ago, created a question with more than 10,000 views. For Number of mapped reads from BAM file

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