Top new questions this week:
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I was working with a given GFF3 file, and I observed that some transcripts have orientation opposite to their transcripts. Here is a snippet: …
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I’m trying to use snakemake to replace some make workflows, but I’m finding that snakemake does not use the file modification time to trigger a rule. Here is my snakefile …
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I use bedtools to convert genomic coordinates (in the form of bed files, chrX x1:x2) to genomic sequence content in the form of fasta files (‘ACGT…G’). The bedtools format for extracting sequence (….
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I have a collection of fasta files, each containing three aligned sequences. I am interested in understanding the distribution of a specific sequence motif PGP, RGP and KGP in all the alignments. I …
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In Pandas, we have pandas.options.display to adjust how a DataFrame should be displayed when printed. I wonder if PyRanges has a …
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I am in the process of creating a bioinformatics pipeline and I am currently trying to setup the AWS infrastructure for which it will run. The script I am running to setup the AWS batch job looks like …
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I am new to using both DESeq2 and EdgeR in Bioconductor used for transforming my RNA expression data. However, I am struggling to understand their specific purpose, differences between them and …
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Greatest hits from previous weeks:
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In a previous post I asked Why do NEB adapters have non-complementary sequence? Since then, I realized that there is some other sequence in the p5 indexing primer, as well as in the p7 indexing …
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I am writing a python script that requires a reverse complement function to be called on DNA strings of length 1 through around length 30. Line profiling programs indicate that my functions spend a …
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I would like to do easily reproducible analysis using publicly available data from NCBI, so I have chosen a snakemake. I would like to write a single rule, that …
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I am trying to install DESeq2 in my Ubuntu with R version 3.5.1. According to the package repository in Bioconductor the version should be 3.5. …
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My annotation file is in .gff format. I would like to convert it to .gtf format or to know if there is a way to directly download the annotation file in .gtf format? I am working on sequences from …
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I apologize for this very basic question. With @Michael G.’s help, I have been learning how to use RAxML to build a phylogenetic tree (How to define an outgroup to build a robust amino acid tree) and …
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I want to convert my gff3 annotation files to genbank format for use in Mauve. I found the seqret tool here www.ebi.ac.uk/Tools/sfc/emboss_seqret/ which can perform this task, but my files (…
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Can you answer these questions?
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as the title says I´m trying to run Bionanos HybridScaffolding from the command line rather than using their own software interface. This is commercial software to primarily to identify genomewide …
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I am trying to generate seq.dat and seq.txt files myself, so that I can use them with REMO. I am using …
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I am using SIMCA software to perform multivariate analysis and want a VIP scores plot in R as shown below. which package is used for this type of plot (image retrieved from Google-images)??
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