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User: Renesh

gravatar for Renesh
Renesh • 1.2k
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Location:
United States
Last seen:
1 week, 6 days ago
Joined:
3 years, 9 months ago
Email:
r******@gmail.com

I am working as postdoctoral research associate at Texas A&M University. I have involved in several Bioinformatics projects, from small to large scale sequence analysis to address abiotic and biotic stresses in plants (Cotton, Sugarcane, Rice, Potato, Tomato, Spartina etc.). I have largely applied Next generation sequencing (NGS) RNA-seq approach to study molecular mechanisms and transcriptional regulation under various abiotic and biotic stresses in a model and non-model plant species. Additionally, I have developed algorithms and software pipeline for efficient analysis for large scale biological data generated from NGS instruments.

Posts by Renesh

<prev • 172 results • page 1 of 18 • next >
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Comment: C: Gene expression units explained: RPM, RPKM, FPKM and TPM
... Can you please explain, where I am wrong in TPM calculation? If you read the paper, it clearly says, T is the total number of transcripts sampled by total sequenced reads. Please, let me know where I am wrong. ...
written 4 months ago by Renesh • 1.2k
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Comment: C: FPKM threshold and filter
... Filter out all transcripts with FPKM variance less than one across all samples/conditions ...
written 8 months ago by Renesh • 1.2k
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Comment: C: installing perl packages.
... You should also try with `yum install` to install the perl packages like `yum install perl-Parallel-ForkManager-1.190.0-1.mga7.noarch` `yum install perl-Tie-IxHash-1.230.0-6.mga6.noarch` `yum install perl-Config-General-2.630.0-1.mga7.noarch` Note: you need to have root permission to install th ...
written 8 months ago by Renesh • 1.2k
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Comment: C: installing perl packages.
... Which Linux you have? ...
written 8 months ago by Renesh • 1.2k
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Answer: A: installing perl packages.
... You can use `capnm` to install the Perl packages. You can type following command on window, Linux, Mac terminal to install `cpanm` `cpan App::cpanminus` After installing `cpanm` use follwing command to install Perl modules, `cpanm Config::General ` Source: http://www.cpan.org/modules/INSTALL.ht ...
written 8 months ago by Renesh • 1.2k
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Comment: C: Is Bio.SeqIO.write() sequential for fastq format?
... Looks like your code is incomplete. Where is panda dataframe object defined? ...
written 8 months ago by Renesh • 1.2k
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Comment: C: How to quantify the overlapping reads in paired-end DNA sequencing to check the
... The term fragment length from BAM file corresponds the total size covered by paired-end reads which may or may not equal to insert size. ...
written 8 months ago by Renesh • 1.2k
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Comment: C: How to quantify the overlapping reads in paired-end DNA sequencing to check the
... https://drive.google.com/file/d/0B3SqUxkB3WxnRWtZbldlOHhZNHM/view?usp=sharing ...
written 8 months ago by Renesh • 1.2k
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Answer: A: How to quantify the overlapping reads in paired-end DNA sequencing to check the
... https://drive.google.com/file/d/0B3SqUxkB3WxnRWtZbldlOHhZNHM/view?usp=sharing ...
written 8 months ago by Renesh • 1.2k
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Answer: A: How to quantify the overlapping reads in paired-end DNA sequencing to check the
... Yes, you can do this with alignment BAM/SAM file. You can extract the record for concordant alignment `YT:Z:CP` from SAM/BAM file. Once you have concordant alignment, you can look for field 9 in SAM/BAM file. Field 9 (9th column) represents the fragment length of paired-end sequences. From here, yo ...
written 8 months ago by Renesh • 1.2k

Latest awards to Renesh

Great Question 3 months ago, created a question with more than 5,000 views. For Gene expression units explained: RPM, RPKM, FPKM and TPM
Epic Question 3 months ago, created a question with more than 10,000 views. For Extract specific patter from string in MySQL:
Appreciated 7 months ago, created a post with more than 5 votes. For A: Does read-depth refer to a fold?
Popular Question 7 months ago, created a question with more than 1,000 views. For Cufflink p-value using blind dispersion method
Popular Question 7 months ago, created a question with more than 1,000 views. For How to use seek() with Biopython SeqIO object
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Masters Ideas in Computer Science that tackles Bioinformatics Problem
Scholar 8 months ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Scholar 8 months ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Guru 8 months ago, received more than 100 upvotes.
Scholar 9 months ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Scholar 9 months ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Scholar 9 months ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Scholar 9 months ago, created an answer that has been accepted. For A: Is there a way to know sequences length when querying ENA programmatically?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Masters Ideas in Computer Science that tackles Bioinformatics Problem
Autobiographer 9 months ago, has more than 80 characters in the information field of the user's profile.
Great Question 17 months ago, created a question with more than 5,000 views. For AttributeError: 'str' object has no attribute 'next'
Popular Question 17 months ago, created a question with more than 1,000 views. For Cufflink p-value using blind dispersion method
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Masters Ideas in Computer Science that tackles Bioinformatics Problem
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: How do you organize your articles?
Great Question 19 months ago, created a question with more than 5,000 views. For AttributeError: 'str' object has no attribute 'next'
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: venn diagram for gene lists using R
Popular Question 2.6 years ago, created a question with more than 1,000 views. For AttributeError: 'str' object has no attribute 'next'
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: venn diagram for gene lists using R
Centurion 3.3 years ago, created 100 posts.
Scholar 3.3 years ago, created an answer that has been accepted. For A: Does read-depth refer to a fold?
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