User: krushnach80

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krushnach80810
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Posts by krushnach80

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Comment: C: How to find the differences in aligned bam files
... if you need to do PCA or clustering take rlog values which i did after running it in deseq2 ...
written 4 weeks ago by krushnach80810
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Comment: C: How To Do Alignment, Stop Codon Removal And Dn/Ds Calulation In One Go?
... I tried with dummy data set it worked but in the actual data set it not working when i run to calculate dn/ds ...
written 7 weeks ago by krushnach80810
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Comment: C: Renaming fasta headers according to a matching name list
... seqkit is a life saver ...
written 7 weeks ago by krushnach80810
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Comment: C: make fasta sequence which is multiple of three
... thanks will look into it trimAI ...
written 7 weeks ago by krushnach80810
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Comment: C: make fasta sequence which is multiple of three
... "You first have to align them and subsequently remove unaligned parts (rather than adding bases!!" I would be interested in doing this how to do this? Since i was trying to do this "If you're intending to run it through PAML to do dNdS " but again the multiple of 3 errors comes. ...
written 7 weeks ago by krushnach80810
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Comment: C: ggtree: phylogenetic tree visualization and annotation
... i have a tree I wanted to label the tree with external annotation. How to do that I been looking at the manual but not clear. I have made an annotation file which has the tip label and its associated data which i want to overlay on my final plot..Any example you can cite in your manual? ...
written 9 weeks ago by krushnach80810
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Comment: C: 16s rna meta-genomics analysis
... Actually we started using that epi2me and WIMP when we had less sequence since that happens all in the server side it takes a lot of time then only we started looking how to do locally. "what region you are looking at from 16S " This I will update ...
written 12 weeks ago by krushnach80810
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Comment: C: 16s rna meta-genomics analysis
... No these are not degenerate primers . How to go about it since there are about 1962 fastq files under each barcoding how to go about it. Should I merge all the fastq files and proceed? ...
written 12 weeks ago by krushnach80810
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Comment: C: 16s rna meta-genomics analysis
... surely i will use that but right now Im in pre processing step of the data I will find out about the primers and update ...
written 12 weeks ago by krushnach80810
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Comment: C: 16s rna meta-genomics analysis
... I will have to find out what primer we have used ...
written 12 weeks ago by krushnach80810

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