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I have two FASTAs/assemblies of the same species, but the bases are somewhat different. I would like to explore this. What tools/methods exist to compare two FASTAs and see...
Asked on 02/18/2021 by EB2127
4 answerI am trying to use optitype on an HPC without docker support or sudo privileges. A search brought me https://github.com/researchapps/optitype and https://github.com/nf-core/hlatyping. I tried...
Asked on 02/17/2021 by SophistRS
0 answerI have two pandas Dataframes, using python3.x:import pandas as pddict1 = {0:['chr1','chr1','chr1','chr1','chr2'], 1:[1, 100, 150, 900, 1], 2:[100, 200, 500, 950, 100], ...
Asked on 02/15/2021
4 answerI've seen two uses of this term that seem to refer to completely different phenomena. Is my understanding correct?In Jain et al. "Active promoters give rise to false positive ‘Phantom...
Asked on 02/13/2021 by eric_kernfeld
1 answerMy understanding from this page https://www.biostars.org/p/272364/ is that it's related to 'High Scoring Pairs', which are in turn related to the way BLAST works. I'm still not...
Asked on 02/12/2021
0 answerI would like to compare mutational signatures1 in patients from different studies, however some studies are based on exome seq (i.e. ~20,000 coding variants) and some are from whole genome...
Asked on 02/12/2021 by jared_mamrot
2 answerAfter discovering a few difficulties with genome assembly, I've taken an interest in finding and categorising repetitive DNA sequences, such as this one from Nippostrongylus brasiliensis [each base is colour-coded...
Asked on 02/11/2021 by gringer
2 answerI have a list of HGNC gene symbols, I am looking to get the gene length of each gene. Although I also describe these genes with lots of UCSC datasets...
Asked on 02/11/2021 by DN1
1 answerI am doing a differential gene expression analysis to find out genes that are differentially expressed in one cell type from the lung in two conditions, control and idipathic pulmonary...
Asked on 02/10/2021
0 answerI have a read count data (RNAseq) and want to perform quantile normalization. Could you please help me how to do it. I tried some scripts in R but it...
Asked on 02/08/2021
3 answerGet help from others!
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