Moderator: venu

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venu5.3k
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Posts by venu

<prev • 661 results • page 1 of 67 • next >
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Answer: C: Find consensus overlap between many bed files
... > Maybe I should just cat all the bed files together and merge them? You can do that. But there is also `multiIntersect`. Check [here][1] [1]: https://www.biostars.org/p/13516/ ...
written 18 days ago by venu5.3k
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Answer: A: Are there any journals that accept short transcriptome announcements?
... There is [nature scientific data][1]. I think this suits your requirements. Check couple of papers from that journal, you will get an idea how to proceed with your data. [1]: https://www.nature.com/sdata/ ...
written 4 weeks ago by venu5.3k
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Answer: C: Expanding Genomic Coordinates Using Bedtools
... There are many working solutions. But as you mentioned bedtools, here is how you do it cat file.bed | windowMaker -b - -w 1 ...
written 4 weeks ago by venu5.3k
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Comment: C: ATAC-seq DE analysis
... +1. I completely forgot about multicov function. Thanks for adding. ...
written 4 weeks ago by venu5.3k
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Comment: C: ATAC-seq DE analysis
... The issue with `bedtools` is one can not input multiple bam files at once. With `multiBamSummary` from deeptools, you can input as many BAM files as possible, it will generate one counts table for all BAMs. ...
written 4 weeks ago by venu5.3k
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Comment: C: ATAC-seq DE analysis
... HT-seq or featureCounts are not really suitable (tedious work to prepare an input format with bed regions) for ChIP/ATAC data. Use `bamCoverage` or `multiBamSummary` from `deeptools`. All you need is BAMs and a bed file. ...
written 4 weeks ago by venu5.3k
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Comment: C: Calculating the hypergeometric value for overlap of two lists of genes
... We have a Bioconductor package for these tasks (includes visualizations): [GeneOverlap][1] [1]: http://bioconductor.org/packages/release/bioc/html/GeneOverlap.html ...
written 5 weeks ago by venu5.3k
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Comment: C: PBS script not able to locate the tool
... Try providing **absolute path** to the tool. This always happens with our cluster. ...
written 5 weeks ago by venu5.3k
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Comment: C: Sampling with replacement from a bam file
... Could you explain what do you mean by `replacement`? ...
written 5 weeks ago by venu5.3k
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Comment: C: Can I determine the machine used for RNA-seq from the .count file extension?
... What do you mean by machine? If you are talking about sequencing machine, ***no it's not super obvious.*** After processing a lot your RNA-seq data looks like what your handling now. That's a raw counts file. I'm guessing `featureCounts` was applied to calculate raw counts (if you meant `machine=to ...
written 5 weeks ago by venu5.3k

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Popular Question 4 days ago, created a question with more than 1,000 views. For Map a protein domain information to a sequence
Scholar 18 days ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
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Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
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Scholar 8 weeks ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Best bioinfo one-liners?
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Sequence extraction from PFAM db with accession ID
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: perl code to extract sequences from multi-line fasta works on all test files but
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: perl code to extract sequences from multi-line fasta works on all test files but
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: perl code to extract sequences from multi-line fasta works on all test files but
Popular Question 4 months ago, created a question with more than 1,000 views. For Sequence extraction from PFAM db with accession ID
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: perl code to extract sequences from multi-line fasta works on all test files but
Popular Question 5 months ago, created a question with more than 1,000 views. For Sequence extraction from PFAM db with accession ID
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Scholar 5 months ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Protein structure distorted after energy minimization using GROMACS
Scholar 5 months ago, created an answer that has been accepted. For A: How to search Pfam DB using list of accessions
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: perl code to extract sequences from multi-line fasta works on all test files but
Appreciated 7 months ago, created a post with more than 5 votes. For A: Best bioinfo one-liners?
Popular Question 7 months ago, created a question with more than 1,000 views. For Sequence extraction from PFAM db with accession ID
Popular Question 8 months ago, created a question with more than 1,000 views. For Sequence extraction from PFAM db with accession ID

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