User: Prakki Rama

gravatar for Prakki Rama
Prakki Rama2.2k
Reputation:
2,210
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Location:
Singapore
Website:
https://asearchforsolu...
Twitter:
Prakki_Rama
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Google Scholar Page
Last seen:
3 weeks, 6 days ago
Joined:
7 years ago
Email:
r***********@gmail.com

Bioinformatics Research Associate 

Linkedin: http://tiny.cc/fn92qy

Posts by Prakki Rama

<prev • 411 results • page 1 of 42 • next >
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Comment: C: How do I access genome coverage using SPADES?
... Thx! BBMAP was very helpful! ...
written 27 days ago by Prakki Rama2.2k
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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 3 months 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 3 months 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 3 months 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 4 months 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 4 months 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 4 months ago by Prakki Rama2.2k
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Comment: C: Missing sequences in local NT database
... I assumed they are same. ...
written 4 months 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 4 months 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 4 months ago by Prakki Rama2.2k • updated 4 months ago by lieven.sterck3.9k

Latest awards to Prakki Rama

Great Question 5 months ago, created a question with more than 5,000 views. For Meaning of Chromatin state
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: [Noob Doubt] Mapping and Annotation.
Popular Question 12 months ago, created a question with more than 1,000 views. For How to generate AGP format using contigs and scaffolds
Popular Question 13 months ago, created a question with more than 1,000 views. For How to generate AGP format using contigs and scaffolds
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: [Noob Doubt] Mapping and Annotation.
Popular Question 15 months ago, created a question with more than 1,000 views. For How to generate AGP format using contigs and scaffolds
Epic Question 17 months ago, created a question with more than 10,000 views. For Aligning Reads To A Reference Transcriptome
Popular Question 18 months ago, created a question with more than 1,000 views. For How to generate AGP format using contigs and scaffolds
Librarian 21 months ago, created a post with more than 10 bookmarks. For Assessing The Quality Of De Novo Assembled Data
Appreciated 21 months ago, created a post with more than 5 votes. For A: Assessing The Quality Of De Novo Assembled Data
Epic Question 21 months ago, created a question with more than 10,000 views. For Assessing The Quality Of De Novo Assembled Data
Student 21 months ago, asked a question with at least 3 up-votes. For Assessing The Quality Of De Novo Assembled Data
Popular Question 22 months ago, created a question with more than 1,000 views. For Meaning of Chromatin state
Popular Question 22 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 23 months ago, created a question with more than 1,000 views. For #Reads Per Contig Information From Assemblies Other Than Velvet
Commentator 23 months ago, created a comment with at least 3 up-votes. For C: samtools idxstats on indexed BAM failed
Great Question 24 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 2.3 years ago, created a post with more than 20 followers. For Assessing The Quality Of De Novo Assembled Data
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Quickest way to extract subset of reads from huge fastq file
Scholar 2.5 years ago, created an answer that has been accepted. For A: RNAseq: remove contaminants before or after mapping reads?
Appreciated 2.5 years ago, created a post with more than 5 votes. For Assessing The Quality Of De Novo Assembled Data
Librarian 2.5 years ago, created a post with more than 10 bookmarks. For Assessing The Quality Of De Novo Assembled Data
Epic Question 2.6 years ago, created a question with more than 10,000 views. For Number of mapped reads from BAM file

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