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Search: Posts Made By: peerah
Forum: Bioinformatics 02-15-2017, 03:38 PM
Replies: 126
Views: 45,632
Posted By peerah
Hi Brian! I have a question: I am working on a...

Hi Brian! I have a question: I am working on a fungal ITS metagenomic amplicon library with a pretty wide variation in sizes (200-500 bp). We are doing 2x300, and my second reads are a little bit...
Forum: Bioinformatics 10-25-2016, 08:45 PM
Replies: 0
Views: 599
Posted By peerah
Unhappy Discrepancy in plasmid and transposons copy number estimation using WGS vs qPCR

We are trying to estimate plasmid copy number in a bacterium by mapping Illumina reads on corrected PacBio contigs and comparing read coverage between the chromosomal and plasmid contigs. Chromosome...
Forum: Illumina/Solexa 05-19-2016, 12:16 PM
Replies: 0
Views: 826
Posted By peerah
Unhappy Copy number determination using sequencing coverage

Hi! We are trying to figure out plasmid copy number for a bacterial organism (Klebsiella pneumoniae) and this was how we approached it by NGS:

1. Genomic sequencing from same bacterium using MiSeq...
Forum: Bioinformatics 03-23-2015, 08:35 AM
Replies: 2
Views: 995
Posted By peerah
BLAST for sequences that are more distantly related

Hi all,

Is there a way to set up NCBI online BLAST to look for sequences that are more distantly related to a subject sequence and have them show up within the top 100? I tried tweaking some...
Forum: Bioinformatics 01-13-2015, 09:17 AM
Replies: 3
Views: 1,036
Posted By peerah
Yes. Sorry I forgot to mention that in the first...

Yes. Sorry I forgot to mention that in the first place. Size is about 5 Mbp.
Forum: Bioinformatics 01-13-2015, 09:12 AM
Replies: 3
Views: 1,036
Posted By peerah
Online tool to calculate percent global identity between draft genomes

Hi,

Is there an online tool where I could upload draft genomes (multi-fasta format containing contig sequences) to do a pairwise comparison and come up with a global percent identity? I tried...
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