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Bioinformatics : Recent Questions and Answers (Page 27)

Find answers to your questions about Bioinformatics or help others by answering their Bioinformatics questions.

SLURM script for running RSEM star fails

If you have worked on cluster with submitting jobs, please help me in resolving the following error. I am running rsem pipeline to generate star index. In principal STAR requires...

Asked on 04/24/2021 by Angelo

0 answer

Genomic relationship matrix explanation

I am seeking the definition of the genetic distance matrices used in genomic prediction.What is the difference between a Rodger distance and kinship matrix?what people mean when they talk about...

Asked on 04/21/2021

0 answer

What is the best way to start for analysing DNA methylation TGCA datasets using R? I want to learn but I'm a novice

I am relatively new to programming and only have a basic knowledge base for R. I am keen on learning how to manipulate DNA methylation arrays for analysis related to...

Asked on 04/21/2021 by Andrew Scarborough

0 answer

How does DeepVariant construct RGB images from DNA sequences?

DeepVariant is a pipeline to call genetic variants from DNA sequencing data. A major step, before feeding the CNN, is to translate these DNA sequences into images....

Asked on 04/18/2021

2 answer

Finding annotated counterpart after BLASTn with efetch (Biopython)

I am creating a pipeline for the identification of unknown transcripts. After a local BLASTn search of the transcripts, I have a large list of the respective hits with different...

Asked on 04/18/2021 by MWP

0 answer

Is identity calculated for jackhmmer run locally?

Having trouble finding this, not sure if the -o flag gives us this by default. Sorry if this is a silly question....

Asked on 04/16/2021

0 answer

Fastq: how can I check if they are from DNA or RNAseq data?

I have (gave me) Illumina fastq files and I do not know if they are DNAseq or RNAseq data. How can I check this? I do not have any report...

Asked on 04/15/2021 by Emma Athan

2 answer

ATAC seq density calculation

This paper Fig2bb Changes of chromatin accessibility in AMD (n = 14) relative tonormal (n = 11) in all retina samples. Each dot represents oneATAC-Seq peak. Blue line in...

Asked on 04/15/2021

2 answer

Identify novel protein using Resfam

I am doing a functional metagenomic study. I did the annotation of protein sequences using HMMER against the Resfam database*. The publication is here...

Asked on 04/15/2021 by ahmedbar

0 answer

How do I Read a Sam File into a String Using ifstream in C++?

I am trying to read a .sam file into a single string in C++. My end goal is to read this string into a vector, where tabs indicate separations between...

Asked on 04/15/2021

0 answer

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