User: Surya Saha

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Surya Saha250
Reputation:
250
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Location:
NY
Twitter:
@SahaSurya
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1 month, 2 weeks ago
Joined:
7 years, 9 months ago
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Posts by Surya Saha

<prev • 21 results • page 1 of 3 • next >
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Comment: C: PBJelly error at mapping level
... This is due to the -- prefix for parameters in blasr 5.1 instead of -. Please see https://sourceforge.net/p/pb-jelly/discussion/pbjtiks/thread/7657e087/ You can run blasr on the command line after modifying the parameter calls appropriately to generate the .m4 file. And yes, this should be fixed in ...
written 2.6 years ago by Surya Saha250
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Answer: A: Tools To Find Gene Ontology Term Enrichment
... Just wanted to add a note that DAVID has not been updated since [2010][1] so should not be used. See [preprint][2] for more detailed discussion. [1]: https://david.ncifcrf.gov/forum/viewtopic.php?f=10&t=807 [2]: http://biorxiv.org/content/early/2016/04/19/049288 ...
written 2.7 years ago by Surya Saha250
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Answer: A: Hierarchy of repeat classes from repeatmasker
... You should be able to get the repeat hierarchy from the RepeatMaskerLib.embl file that is distributed as a part of the RepBase library used for this annotation (RepeatMasker Library db20140131).  RepBase libraries are available from GIRI after free registration. http://www.girinst.org/server/RepBas ...
written 3.8 years ago by Surya Saha250
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Answer: A: SOL-genomics programming API to retrieve data from server
... We do not offer an API for SGN web services although we may consider that in the future is there is sufficient demand. ...
written 4.2 years ago by Surya Saha250
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Comment: C: SOL-GENOMICS: Find in which gene a specific region belongs to.
... We do not offer an API for SGN web services although we may consider that in the future is there is sufficient demand and capacity. ...
written 4.2 years ago by Surya Saha250
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Answer: A: SOL-GENOMICS: Find in which gene a specific region belongs to.
... Hello Frank, There is a problem with your search string. You are using "SL2.40:50532..53532" which has 2 issues. ITAG2.4 is using the latest tomato genome build 2.50. The chromosome is also missing. An example of a correct search term is "SL2.50ch08:2626000..2648999". In case you are interested in ...
written 4.2 years ago by Surya Saha250
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Comment: C: Coordinates Of Non Synonymous Snps
... Thanks anyways. Other folks I have spoken to have been stumped too. ...
written 5.3 years ago by Surya Saha250
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Comment: C: Coordinates Of Non Synonymous Snps
... I have the complete nucleotide sequence of genes (avg 840 bp) for both genomes from Refseq. I also have the ids of orthologous gene pairs from both genomes, if that helps. That crazy idea crossed my mind too :-) But thats a last resort. I was thinking of using a simple blast to compare the pair and ...
written 5.3 years ago by Surya Saha250
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Comment: C: Coordinates Of Non Synonymous Snps
... Thank you for the reply. Methods suggested work off a read mapping input file, like most tools available today. What I have are two complete genes that need to be compared for non-synonymous SNPs. ...
written 5.3 years ago by Surya Saha250
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Coordinates Of Non Synonymous Snps
... I have a set of homologous gene pairs from two complete bacterial genomes. I also have the whole chromosome and GFF files of gene locations. I want to find the coordinates for non-synonymous SNPs in each gene relative to its homolog. Is there a tool where I can feed the gene pairs or even better c ...
bacteria coordinates snp written 5.3 years ago by Surya Saha250

Latest awards to Surya Saha

Prophet 10 months ago, created a post with more than 20 followers. For Combining The Paired Reads From Illumina Run
Epic Question 22 months ago, created a question with more than 10,000 views. For Combining The Paired Reads From Illumina Run
Good Question 22 months ago, asked a question that was upvoted at least 5 times. For Combining The Paired Reads From Illumina Run
Epic Question 22 months ago, created a question with more than 10,000 views. For Discrepancy In Samtools Mpileup/Depth And Bedtools Genomecoveragebed Counts
Appreciated 2.6 years ago, created a post with more than 5 votes. For Discrepancy In Samtools Mpileup/Depth And Bedtools Genomecoveragebed Counts
Good Question 2.6 years ago, asked a question that was upvoted at least 5 times. For Discrepancy In Samtools Mpileup/Depth And Bedtools Genomecoveragebed Counts
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Coordinates Of Non Synonymous Snps
Great Question 3.0 years ago, created a question with more than 5,000 views. For Discrepancy In Samtools Mpileup/Depth And Bedtools Genomecoveragebed Counts
Appreciated 3.0 years ago, created a post with more than 5 votes. For Combining The Paired Reads From Illumina Run
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Coordinates Of Non Synonymous Snps
Great Question 4.0 years ago, created a question with more than 5,000 views. For Discrepancy In Samtools Mpileup/Depth And Bedtools Genomecoveragebed Counts
Scholar 4.2 years ago, created an answer that has been accepted. For A: SOL-GENOMICS: Find in which gene a specific region belongs to.
Student 4.7 years ago, asked a question with at least 3 up-votes. For Discrepancy In Samtools Mpileup/Depth And Bedtools Genomecoveragebed Counts
Student 4.7 years ago, asked a question with at least 3 up-votes. For Combining The Paired Reads From Illumina Run
Teacher 5.8 years ago, created an answer with at least 3 up-votes. For A: Bwa Commands
Popular Question 5.8 years ago, created a question with more than 1,000 views. For Discrepancy In Samtools Mpileup/Depth And Bedtools Genomecoveragebed Counts
Popular Question 7.8 years ago, created a question with more than 1,000 views. For Combining The Paired Reads From Illumina Run

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