User: zuhaibzulfiqarahmed
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Posts by zuhaibzulfiqarahmed
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... Hello,
I got a local instance of galaxy on my computer, and wanted to run a differential expression analysis for some samples of human RNA-seq data. I've managed to download the fastq reads for the samples and I've downloaded and indexed the human genome using HISAT2 index builder. But when I tried ...
written 8 months ago by
zuhaibzulfiqarahmed • 0
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... Thank You! The way I was thinking of doing it is to pool all the GO terms from all results, and take the top 3 or 4, as a representative annotation for the gene. For example, for the mgsA gene has results in cows, humans, myobacterium, sacchromyces, etc. So take all the GO annotations from all those ...
written 12 months ago by
zuhaibzulfiqarahmed • 0
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... @Jean-Karim Heriche
Thanks for the reply. So for example, the mgsA gene in E coli would have similar annotations as the mgsA gene in humans? ...
written 12 months ago by
zuhaibzulfiqarahmed • 0
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... Hello,
I'm writing a small program that takes in a list of Uniprot gene names (and organisms of interest), and returns a visual representation of the GO terms associated with that list of genes in the specified organisms.
I've run into an issue though. What if Uniprot doesn't have the GO terms for ...
written 12 months ago by
zuhaibzulfiqarahmed • 0
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... Hello,
So I'm using Prokka to annotate the Borrelia Burgdorferi reference genome (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/008/685/GCF_000008685.2_ASM868v2)
So once I ran prokka on the .fna file, I used the following command to get the list of genes
#Gets the list of genes, and puts th ...
written 14 months ago by
zuhaibzulfiqarahmed • 0
• updated
14 months ago by
h.mon ♦ 29k
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... Thank You. But is it safe to assume that the newest assembly is the most accurate one? I'd actually like to explore what sort of genes are on the plasmid, but some assemblies only show one chromosome. So should I go for another assembly? ...
written 14 months ago by
zuhaibzulfiqarahmed • 0
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... Hello,
I'm working on a final project for my genomics course. I'd like to analyze the genomes for a few species of Borrelia. However, the assemblies of the genomes seem to be very inconsistent. For example, for Borrelia afzelii, one assembly has 6 chromosomes and plasmids, and another has 10. Anoth ...
written 14 months ago by
zuhaibzulfiqarahmed • 0
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