User: mrals89

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mrals8920
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United States
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3 days, 22 hours ago
Joined:
5 years, 5 months ago
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Posts by mrals89

<prev • 18 results • page 1 of 2 • next >
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Comment: C: what is the best way to calculate significant differences in tss profiles?
... Echoing ATpoint for a second, you are trying to test for differences between singletons, which isn't possible base-by-base between singletons. You require replicates measurements of coverage in order to do a KS-test or something similar. A p-value isn't a very strong statistic, since 'coverage' valu ...
written 23 days ago by mrals8920
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Comment: C: Linear Modelling In Systems Biology help
... I think you should start with the biological process you want to model. If you don't have something you wish to model, then you should start with 'Mathematical Biology' which is a great introduction to application of growth rates and system dynamics to biology. A 2x1 or 1x1 system may *seem* trivial ...
written 25 days ago by mrals8920
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Comment: C: Is it possible to transfer a local instance of Galaxy (from my computer) to Clou
... What is the command line you're using for hisat? Also, moving the indices, references, and tools into AWS is a considerable effort. If you're looking to just run a one-off analysis, you're better off launching a cloud instance, SSH-ing into the instance and performing your analysis there than settin ...
written 26 days ago by mrals8920
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Answer: A: Distance of promoter from TSS
... Hello there. I'd say that you're focusing your efforts on a single gene. The question you asked is, how unlikely is the promoter sequence's distance? That is a bioinformatics question certainly. To 'guestimate' whether this anwer is reasonable you'd need data on promoter locations across many genes, ...
written 26 days ago by mrals8920
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Comment: C: Any packages to validate FASTA file?
... If you need empty records to be considered invalid, maybe you could issue a pull request to biopython ...
written 6 months ago by mrals8920
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Comment: C: Modern software for whole genome alignment visualization
... Compare in what way, sir? Are you looking at rearrangements? CNVs? Or are you interested in homology and sequence features? ...
written 15 months ago by mrals8920
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Answer: A: Looking for a local alignment library with certain features
... From your comment to @ATpoint, it seems like you're looking for 'long' read alignment algorithms. I'd suggest BWA-mem for that (it seems to be the conventional wisdom). But OP, it's not clear why you 'cant have indexes or many I/O operations.' Because BLAST uses indices!! I can't tell if you're tr ...
written 15 months ago by mrals8920
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Comment: C: Modern software for whole genome alignment visualization
... I think there's a separation of concerns issue here OP. Genome browsers are typically responsible for loading BAM, fasta, and BED annotations, maybe vcfs. They are a data exploration application. Ability to extract variants... you mean predict from the BAM files? Or you mean export the loaded vcfs ...
written 15 months ago by mrals8920
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Comment: C: How to download sequences of one gene from all individuals from 1000 genome (pha
... This is a simpler approach to study the SNPs than just slicing the gene from the BAM files or assemblies, OP. ...
written 15 months ago by mrals8920
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Comment: C: aligning with bacterial genome
... Poly A selection is quite common, but OP didn't mention his protocol. Also, poly-A selection biases your samples away from other human RNA species that don't have the tail. You don't need *any* special protocol for bacterial RNA-seq if you're working in an RNAse free environment. Therefore, bacteria ...
written 15 months ago by mrals8920

Latest awards to mrals89

Popular Question 2.2 years ago, created a question with more than 1,000 views. For Does Every Read In Paired-End Sam File Have The 0X0001 Flag?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Directional Rnaseq: Which Mapping Software For Bacteria?

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