User: Anand Rao

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Anand Rao190
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7 hours ago
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7 years, 4 months ago
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Posts by Anand Rao

<prev • 111 results • page 1 of 12 • next >
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Answer: A: mummerplot for genome self alignment NOT yielding full length diagonal graph
... ![enter image description here][1]Solved it: it was the syntax that was wrong (for MUMMER version 4) Plus. I've chosen to use mummer rather than nucmer for step 1, as follows: mummer -mumreference $IN $IN -l $MIN_CONTIG_LEN -threads 12 > $MUMS Followed by step 2: mummerplot mummerplot ...
written 12 days ago by Anand Rao190
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mummerplot for genome self alignment NOT yielding full length diagonal graph
... I am trying to obtain the classical diagonal plot for genome self alignment For this, I am trying out my MUMMER syntax with a slightly processed Arabidopsis thaliana genome that can be downloaded from https://ufile.io/93muh Syntax records are as shown below **STEP 1 - nucmer (2 variations in synt ...
mummer genome alignment mummerplot nucmer written 13 days ago by Anand Rao190
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Comment: C: CD-HIT results without sorting by length
... Thanks for confirming. Cheers and HNY! ...
written 17 days ago by Anand Rao190
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Comment: C: CD-HIT results without sorting by length
... Thank you! It explains why I could not remember the sorting step clearly, or find any utility that performs it explicitly. HNY! Cheers! ...
written 17 days ago by Anand Rao190
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CD-HIT results without sorting by length
... Greetings! AFAIK, CD-HIT requires sorting by length before performing the clustering step. Am I right? If yes, please read on. If not, then there is no question :) I used CD-HIT based clustering to remove 100% identical sequences after retaining just one representative, and then proceed with a BLA ...
length cd-hit clustering sort written 18 days ago by Anand Rao190
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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 3 months ago by Anand Rao190
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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 4 months ago by Anand Rao190
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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 4 months ago by Anand Rao190
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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 4 months ago by Anand Rao190 • updated 4 months ago by Alex Reynolds27k
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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 4 months ago by Anand Rao190

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Popular Question 9 days ago, created a question with more than 1,000 views. For Database for plant ploidy
Student 9 days ago, asked a question with at least 3 up-votes. For Visualize multiple GFF files
Scholar 12 days ago, created an answer that has been accepted. For A: REAPR run error
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Database for plant ploidy
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Popular Question 3 months ago, created a question with more than 1,000 views. For map gene gain loss on species tree
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Popular Question 8 months ago, created a question with more than 1,000 views. For Database for plant ploidy
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