User: sridhar56

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sridhar56100
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Posts by sridhar56

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Comment: C: 16S reads comparing
... You should take a look at DADA2, will be useful for your comparison. This paper will give you an idea on how the data can be comparable: https://www.nature.com/articles/ismej2017119 ...
written 12 months ago by sridhar56100
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Comment: C: How to prep an input (nexus) file for BEAST/BEAUTi?
... I am not sure if you have to remove the recombination. Isnt the recombination information useful to help you identify evolution and understand the phylodynamics? I have created a Multiple Sequence Alignment file and then done the analysis in the past. ...
written 12 months ago by sridhar56100
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Comment: C: Error about Count_fasta.pl
... It seems to be working fine for me. I took a subset of the file (your example file is huge) and ran the program you mentioned. You should probably save your file again and see if it works. 300:399 17 400:499 24 500:599 35 600:699 27 700:799 42 800:899 28 900:9 ...
written 15 months ago by sridhar56100
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Comment: C: Error about Count_fasta.pl
... If it works on other FASTA files, I would guess there is something wrong with the FASTA file you are working with. Did you check if your FASTA file has sequences? Did you check if it is formatted correctly? The following error message: Illegal division by zero at /home/aubhxz/Count_fasta.pl line 1 ...
written 15 months ago by sridhar56100
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Comment: C: Good quality mock community?
... Have you tried BEI resources? [BEI resources][1] [1]: https://www.beiresources.org/Home.aspx ...
written 16 months ago by sridhar56100
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Comment: C: Normalisation of Microbiome Data for Beta Diversity Analysis
... Have you tried phyloseq for the same purpose? ...
written 17 months ago by sridhar56100
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Comment: C: SRAtoolkit: error while running sam-dump
... I just ran your command on a Ubuntu 16.04 and I was able to download the file. Maybe something wrong with your computer? ...
written 17 months ago by sridhar56100
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Comment: C: Can IonProton sequencing data be processed using BWA + FreeBayes or CLC?
... I just checked CLC Genomics Workbench and see that you can import Ion torrent data. It should be able to handle the data and I would assume you would have to filter out the homopolymers in your data. I would assume you can also use the BWA, Freebayes to work with Ion torrent data, it should not be ...
written 20 months ago by sridhar56100
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Comment: C: UPGMA method when tree leaves have different known ages
... For the dataset being considered here, i.e., 5 to 50 sequences (leaves) I think it can be processed quickly, of course a server would be advantageous. I have had datasets with 200 to 400 sequences and was able to run them in 24 hours for 200 million generations. Also for the purposes of the year sep ...
written 20 months ago by sridhar56100
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Comment: C: Assemble Genome from several samples
... I am sorry to sound harsh (rude) here, the data you are talking about seems a complex dataset. You cannot make a generic pipeline for something which has not been classified as a genome/new species. Also, my apologies but I would encourage you to care about the species you are working with. Every s ...
written 21 months ago by sridhar56100

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Commentator 24 months ago, created a comment with at least 3 up-votes. For C: Many to Many alignment of Large number of sequences

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