User: Anand Rao

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Anand Rao160
Reputation:
160
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Trusted
Location:
United States
Last seen:
1 week, 6 days ago
Joined:
7 years, 1 month ago
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Posts by Anand Rao

<prev • 106 results • page 1 of 11 • next >
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Choosing tool for DNA secondary structure stem-loop prediction
... I am looking to identify a stem-loop DNA secondary structure in genomic DNA (not RNA) sequences. This structure is usually ~ 10nt from the 3' terminus, and it is usually ~15-20nt long. There seem to be > a dozen options to predict secondary structure in DNA (like at this page: https://omictools ...
software secondary stem loop dna written 15 days ago by Anand Rao160
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Comment: C: Merge intervals between but NOT within 2 BED files
... Thank you. I've got to think about this, using real data. Because there is no restriction to separation between elements in real-life B.bed data....Thanks again...Like Ram suggested, I might have to cobble up some code for these customized analyses... ...
written 5 weeks ago by Anand Rao160
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Comment: C: Merge intervals between but NOT within 2 BED files
... Thank you for pointing that out, Alex. I fixed the error above. Look forward to your response. Thanks, in advance. ...
written 5 weeks ago by Anand Rao160
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Merge intervals between but NOT within 2 BED files
... I have BED files for 2 types of coords: A and B. I want to collapse them into intervals where an entry of A is separated from an entry of B by not more than 20, and vice versa. What is **not** acceptable is a merge of coordinates with 2 or more entries from just A or 2 or more entries from just B. ...
bedtools overlap merge bedops written 5 weeks ago by Anand Rao160 • updated 5 weeks ago by Alex Reynolds26k
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Any users of pOrthoDom?
... I am trying to use pOrthoDom which is a wrapper around proteinOrtho, neither of which I have used before. I find user instructions for the latter, not the former. So, I am requesting help from pOrthoDom users in the form of a user manual or experience using this software for inferring protein orth ...
ortholog porthodom proteinortho written 7 weeks ago by Anand Rao160
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Answer: A: Phylogenetic tree from single copy core genes (metazoa proteomes)
... If I understand your question and problem correctly, what might useful and relevant is something like BUSCO - http://busco.ezlab.org/? Which in turn uses the orthologs listed at OrthoDB - https://www.orthodb.org/ At that link, you can see there are 330 BUSCOs i.e. orthologs that are "expected" in a ...
written 9 weeks ago by Anand Rao160
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Comment: C: Phylogenetic tree from single copy core genes (metazoa proteomes)
... Moved my response from comment to answer ...
written 9 weeks ago by Anand Rao160
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Visualize multiple GFF files
... For each of several genomes, apart from the already available fasta sequence and associated GFF3 annotation files, I have also generated 5 additional GFF files for start-stop coordinates of 5 additional types of genomic features. My goal is four-fold in the context of these 6 GFF files and 1 genom ...
overlap gff visualization statistics written 9 weeks ago by Anand Rao160
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Answer: A: bedtools strategy to report both merged AND unmerged intervals
... Thank you, Alex. I tried your syntax, first converting GFF to BED, simply using gff2bed. And then, bedops --merge foo.bed | bedmap --count --echo-map - foo.bed | awk '($1>0)' | cut -f2- | sort-bed - | bedops -n 1 foo.bed - > unmerged.bed I received an error message that reads: > End ...
written 10 weeks ago by Anand Rao160
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bedtools strategy to report both merged AND unmerged intervals
... I have 2 GFF3 files that I want to analyze and report the following: type 1 - merge and report adjacent intervals (up to 2000bp away) coords, using bedtools merge type 2 - report unmerged coords as they are - so intact GFF3 lines from respective files I achieved step 1 simply using bedtools mer ...
bedtools gff3 merge unmerged written 10 weeks ago by Anand Rao160

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Popular Question 18 days ago, created a question with more than 1,000 views. For Database for plant ploidy
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