Tag: CLIP

10 things we learned about microbes in 2021

Take a trip to the marvelous world of microbes, where bacteria breathe electricity, neon-yellow slime molds forage for snacks on the forest floor, and thousands of mysterious viruses hang out in your guts. This year, scientists made a slew of fascinating discoveries about the microscopic organisms living in and all…

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Multiple data points in one r ggplot2 plot ( R, Ggplot2 )

Problem : ( Scroll to solution ) I have two sets of data points that both relate to the same primary axis, but who differ in secondary axis. Is there some way to plot them on top of each other in R using ggplot2? What I am looking for is…

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RStudio AI Weblog: Picture segmentation with U-Internet

Certain, it’s good when I’ve an image of some object, and a neural community can inform me what sort of object that’s. Extra realistically, there is perhaps a number of salient objects in that image, and it tells me what they’re, and the place they’re. The latter process (referred to…

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Piranha Peak-Calling with multiple replicates

Piranha Peak-Calling with multiple replicates 0 I am trying to call RNA-Protein interation peaks by using Piranha software. I have multiple replicates for each experiment and the control data, and I can’t seem to understand how to combine them into one Piranha query. For example, if I was to call…

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Independent and minimal implementations of some reinforcement learning algorithms using PyTorch (including PPO, A3C, A2C, …).

There are implementations of some reinforcement learning algorithms, whose characteristics are as follow: Less packages-based: Only PyTorch and Gym, for building neural networks and testing algorithms’ performance respectively, are necessary to install. Independent implementation: All RL algorithms are implemented in separate files, which facilitates to understand their processes and modify…

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Independent and minimal implementations of some reinforcement learning algorithms using PyTorch

There are implementations of some reinforcement learning algorithms, whose characteristics are as follow: Less packages-based: Only PyTorch and Gym, for building neural networks and testing algorithms’ performance respectively, are necessary to install. Independent implementation: All RL algorithms are implemented in separate files, which facilitates to understand their processes and modify…

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ggplot, drawing multiple lines across facets

ggplot, drawing multiple lines across facets I drew two panels in a column using ggplot2 facet, and would like to add two vertical lines across the panels at x = 4 and 8. The following is the code: library(ggplot2) library(gtable) library(grid) dat <- data.frame(x=rep(1:10,2),y=1:20+rnorm(20),z=c(rep(“A”,10),rep(“B”,10))) P <- ggplot(dat,aes(x,y)) + geom_point() +…

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converting Bam to fastq while removing clipping(hard/soft clip bases)

converting Bam to fastq while removing clipping(hard/soft clip bases) 0 Hello, I want to do some analysis and my raw data is paired-end reads fastq files. So far: I used BWA mem to convert them to Sam file then used samtools to convert to BAM file. My next step is…

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Haplotype divergence supports long-term asexuality in the oribatid mite Oppiella nova

Significance Putatively ancient asexual species pose a challenge to theory because they appear to escape the predicted negative long-term consequences of asexuality. Although long-term asexuality is difficult to demonstrate, specific signatures of haplotype divergence, called the “Meselson effect,” are regarded as strong support for long-term asexuality. Here, we provide evidence…

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Primers trimming from Illumina paired-end reads by BBDuk software

Primers trimming from Illumina paired-end reads by BBDuk software 0 Hi, I’m dealing with Illumina amplicon data. I’d like to apply BBDuk to remove primers from the 5’end of my forward and reverse reads, but have a couple of questions. Could you help me please? How may i indicate in…

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The Best 1105 Python kaggle-ranzcr-clip-public Libraries

Athena is an open-source implementation of end-to-end speech processing engine. Athena is an open-source implementation of end-to-end speech processing engine. Our vision is to empower both industrial application and academic research on end-to-end models for speech processing. To make speech processing available to everyone, we’re also releasing example implementation and…

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Trimmomatic error

Trimmomatic error 1 Hi everyone. I’m trying to trim some read data but i’m getting an error message. This is my input: trimmomatic PE -threads 24 -phred 33 /home/tbeckett/lustre/practice/output_data/ Filtered2S1_L3_R1.fastq.gz /home/tbeckett/lustre/practice/output_data/ Filtered2S1_L3_R2.fastq.gz /home/tbeckett/lustre/practice/output_data/trimmed/ TrimmedFiltered2S1_L3_R1_p.fastq /home/tbeckett/lustre/practice/output_data/trimmed/ TrimmedFiltered2S1_L3_R1_un.fastq /home/tbeckett/lustre/practice/output_data/trimmed/ TrimmedFiltered2S1_L3_R2_p.fastq /home/tbeckett/lustre/practice/output_data/trimmed/ TrimmedFiltered2S1_L3_R2_un.fastq ILLUMINACLIP:NexteraPE-PE.fa LEADING:20 TRAILING:20 MINLEN:60 This is the error i’m getting:…

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The Point of Base Editors: Correcting Point Mutations

Some genome editing systems are highly conspicuous. They introduce double-strand breaks to DNA that attract the attention of cellular mechanisms such as nonhomologous end joining and homology-directed repair. If a genome editing system is so brash as to attempt a sizable insertion of new DNA, homology-directed repair must ensure that…

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removing adaptor

removing adaptor 1 I have two RNAseq datasets, from two different sequencing core facilities – the fastq files they provide already are demultiplexed and trimmed for adaptor. This is the Adaptor content following fastqc-> multiqc . According to the multiqc all files passed the qc for adapter content. So I…

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BSgenomes for HIV viruses

BSgenomes for HIV viruses 0 Dear Biostars users, I wonder if there are BSgenomes available for HIV viruses? I am trying to identify clusters from CLIP-seq data mapping to the HIV genome with wavClusteR. I stuck at one step as below: `require(BSgenome.Hsapiens.UCSC.hg19) wavclusters <- filterClusters( clusters = clusters, highConfSub =…

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getting paired end datasets from SRA

getting paired end datasets from SRA 0 I am searching SRA by keywords like “paired-end”, but the sra-toolkit seems to only download one file (single-end) about 90% of the time. I just want to make sure my commands are all correct: prefetch SRR13310323 fastq-dump -I –split-files –outdir fastq –gzip –skip-technical…

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What’s Wrong With Limiting Transformers To Just Language Models

Three years back, Google introduced Transformer, a novel neural network architecture. Modelled on the self-attention mechanism and best suited for language understanding, transformers could outperform both recurrent and convolutional neural network models.  Transformers perceive the entire input sequences simultaneously. The process depends on transforming one sequence into another, like the…

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Trimming of adapters and indexes

Trimming of adapters and indexes 0 I investigate a protein which binds small DNA (<30 nt) and have a library of these small DNA. I know that adapters and indexes are from this site (5′ adapter has T instead of U). [To reach the page I want to show click…

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