bioinformatics | Utilities written for bioinformatics | Genomics library

I'm currently making a start on using Nextflow to develop a bioinformatics pipeline. Below, I've created a params.files variable which contains my FASTQ files, and then input this into fasta_files channel. The process trimming and its scripts takes this channel as the input, and then ideally, I would output all the $sample".trimmed.fq.gz into the output channel, trimmed_channel. However, when I run this script, I get the following error:

Missing output file(s) `trimmed_files` expected by process `trimming` (1)

The nextflow script I'm trying to run is:

I am working on Next Generation Sequencing (NGS) analysis of DNA. I am using SeqIO Biopython module to parse the DNA libraries in Fasta format. I want to filter the unique clones (unique records) only. I am using the following python code for this purpose.

In bioinformatics we have the bgzip file, which is block-compressed, meaning that you can compress a file (let's say a CSV), and then if you want to access some data in the middle of that file, you can decompress only the middle chunk, rather than the entire file.

As is explained here, Arrow (and therefore Feather v2, the file format) seems to support chunked reads and writes, and also compression. However it isn't clear if the compression applies to the entire file, or if individual chunks can be decompressed. This is my questions: can we separately compress chunks of an Arrow/Feather v2 and then later decompress a single chunk without decompressing everything?

I am carrying out some exercises from a very good online R/bioinformatics course. To this end I am wrangling with data in the form of a 'SummarizedExperiment' object from a Bioconductor package of the same name. The rows consist of gene names and gene expression values; the columns consist of 9 ctrl (control) samples, 9 'drug1' treated samples and 9 'drug5' treated samples. Here is what the table looks like: The task is to regroup data in this dataframe so that CTRL0_1 - CTRL0_9 are placed in a single column, named 'CTRL0'. In the same fashion, new 'DRUG1' and 'DRUG5' named columns are needed consisting of gene expression for each gene in the columns DRUG1_1 - DRUG1_9 and DRUG5_1 - DRUG5_9, respectively. Data are derived from the final question on this webpage: https://uclouvain-cbio.github.io/WSBIM1207/sec-bioinfo.html The task is to generate a ggplot like this: Instead, with my inelegant code I get this: To generate MY plot, I used this code:

I am new to snakemake workflow management and I'm struggling to grasp how the wildcards input works. I tried to do QC of some SRR data but the snakemake is giving the "MissingRuleException error".

my config file(config.yaml) contain the content:

samples: sample.csv

path: /Users/path/Bioinformatics/srr_practice

sample.csv is

I am taking a fourth year bioinformatics course. In this current assignment, the prof has given us a gff file with all the miRNA genes in the human genome annotated as gene-MIR. We are supposed to use grep, along with a regular expression and other command-line tools to generate a list of unique miRNA names in the human genome. It seems fairly straight forward and I understand how to do most of it. But I am having trouble sorting the file and removing the repeated lines. We are supposed to do this in one command line, but I am having trouble doing so.

This is the grep command I used to generate a list of gene-MIR names:

From my instrumentation, I receive two different .tsv files containing my data. The first file contains, among other things, the name of the sample, its position in a 12x8 grid, and its output data. The second file contains average data from replicate sets based off the first text file. I've re-created an example of the two files in these data frames -- I actually read them using the read.table() function.

I have successfully installed Cytoscape.

I am creating a Linkedin job scraper in order of most recent, but I am finding it really difficult to target the 'Most recent' radio button as shown below.

So far, the 'Most relevant' menu is clicked on, but will not click on 'Most recent'. Help would be appreciated I can't seem to figure this one out :/

Code snippet