User: karthic

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karthic100
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Posts by karthic

<prev • 60 results • page 1 of 6 • next >
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Any new recommended protocol for gene prediction, if you have isoseq data??
... Dear all, I would like to get some suggestions/recommendations regarding gene prediction for a repeat rich eukaryote genome. We have pacbio isoseq data for some tissues and also illumina based transcriptomes. Does the availability of isoseq data mandates any new method or I should just follow the ...
isoseq gene prediction pacbio rna-seq written 1 day ago by karthic100
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Comment: C: Strand aware gff3 to protein fasta
... Thanks for your reply. I have used bedtools fasta, I can force strandedness but it outputs only as nucleotide fasta. Not sure about AGAT, going to install. But from the list of program names, I am unable to find the requisite one. ...
written 11 weeks ago by karthic100
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Strand aware gff3 to protein fasta
... Hi everyone, I know there are lots of program which can translate the nucleotide fasta to protein fasta in all 6 frames or the frame we desire. But is there any program which can take genome fasta + gff3 table and give protein fasta as output by taking the strand of each sequence also into consider ...
genome sequence written 11 weeks ago by karthic100
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get summary from last alignments
... Dear all, I have alignment two large genomes using `last`. It has given me a maf output file. Is there any way to get quick summary of the alignment, say how much of genome1 is alignment to genome2?? Thanks, Karthic ...
genome alignment sequence written 7 months ago by karthic100
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maf-swap: error: list index out of range
... Hi Everyone, I am trying to perform alignment between two large genomes of around 1.5G using `last` by following steps from [here][1]. I face the problem when I run the `maf-swap` program on the maf file. maf-swap: error: list index out of range Any suggestions?? Thanks, KK [1]: https://g ...
genome assembly alignment software error written 8 months ago by karthic100
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Unable to redirect mummer log to a file when called inside php
... I have the following mummer command, when run in terminal it redirects both output and error (log) to separate files. mummer -mum Reference.fasta Query.fasta > output.txt 2> err.txt However the same command when called inside a php as below, it only prints output but not error (log). ...
software error sequence next-gen alignment written 9 months ago by karthic100 • updated 9 months ago by Biostar ♦♦ 20
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Comment: C: Highly similar bacterial genomes
... Thank you, I will have a look and see if they suit me. ...
written 17 months ago by karthic100
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Highly similar bacterial genomes
... Hi, I am searching for some bacterial strains or isolates having very high genome similarity as a model to test a program. Since my knowledge in bacterial genomics is very limited, I would really appreciate if someone suggests the genomes, if possible a paper who have done similar kind of work. TI ...
genome bacterial genomes comparative study written 17 months ago by karthic100
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Comment: C: Creating interaction network using cytoscape
... Hi Piyush, you can study PPI using ClusterOne. First submit your proteins to Sting DB and fetch the interaction table. Then submit the interaction table to Cytoscape and run ClusterOne on that. Sample input is below.. node1 interaction node2 combined_score DappuP317081 combined_score Dap ...
written 21 months ago by karthic100
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Comment: C: What is Genome-sequencing?
... I believe the user has copied the text from a manuscript and pasted here and trying to figure out the term "Genome Sequencing" in that text mean!! ...
written 21 months ago by karthic100

Latest awards to karthic

Popular Question 23 months ago, created a question with more than 1,000 views. For Genome size estimation using jellyfish
Popular Question 24 months ago, created a question with more than 1,000 views. For Any methods available to do QC analysis of Pacbio raw data??
Scholar 24 months ago, created an answer that has been accepted. For A: perl script for discarding sequences less than 200 nucleotides before running C
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: perl script for discarding sequences less than 200 nucleotides before running C
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Any methods available to do QC analysis of Pacbio raw data??

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