Genetics

BUSCO installation and run 2 That unil.ch link looks a bit too complicated, these are the commands I ran to get BUSCO via Singularity: Download the image: singularity pull Run the image with example genome.fasta, assuming it’s a genome and a plant: singularity run -B $(pwd):/busco_wd/ busco_v5.2.2_cv1.sif busco -l viridiplantae -m genome -i genome.fasta […]

The biggies are obviously DESeq2, limma and edgeR, but they are massive packages doing some very complex statistics, and also have dependency trees that would need to be considered. Depending on your background, you might want to look into the rtracklayer/GenomicRanges eco-system. While I personally am not a fan, I know they are very popular, […]

Functional enrichment and visualization of metatranscriptomics data 0 Hi, I am new to clusterProfiler. Is it possible to use clusterProfiler for metatranscriptomics DEG data (deseq2)? As i read from yulab-smu.top/clusterProfiler-book/chapter3.html#input-data for unsupported organisms, one need to create TERM2GENE and TERM2NAME file, which according to the guide requires a organism specfic gmt file. My sample is […]

Hello, I am trying to run this command line in the terminal from Mac OS, which is copied from a protocol: FEELnc_codpot.pl –i <unannotated_transcript.fa> -a <mRNA_sequence.fa> -g <reference_genome.fa> -m ’shuffle’ –o <unannotated_transcript> However, I get the following error: command not found, probably because I am not using perl, so I entered: perl FEELnc_codpot.pl which gives […]

I have access to 5′ nascent RNA-seq data that captures transcription initiation information at basepair resolution. For those of you familiar, the data produced is similar to CAGE-seq/5′ PRO-seq/GRO-cap/csRNA-seq. PROBLEM: I would like to compare a promoter in two different conditions and identify initiation sites that are differentially expressed/used between these two conditions. BACKGROUND: I […]

Creating Signature Matrix from SC-RNA Seq data for Deconvolution of Bulk Tissue 0 Hey, I’ve been trying to understand how to create a signature matrix but there’s no tutorials to follow and the papers I’ve found from Cibersort and others lack in detailing step by step. So, can anyone provide some insights on the matter. […]

Hi, I want to append numbers on all headers (gene names), not only duplicates or multiplicates but also unique ones, in FASTA file. Does anyone have solutions? My file is pretty large so I am trying to find some code. Unfortunately, I can not currently run R scripts in our institute server, so I would […]

Gene ontology 0 Hii guys, I would like to represent my gene ontology data in venn diagram. How do I do it? Please help. bn • 69 views • link updated 2 hours ago by Ankit &utrif; 180 • written 4 days ago by Hymavathi • 0 Login before adding your answer. Source link

Interpreting bcftools isec output 1 Hi, I attempted to find overlapping variants across my four panels using bcftools isec -p dir -n=4 <file1.vcf.gz> <file2.vcf.gz> <file3.vcf.gz> <file4.vcf.gz> I got this list of outputs: 0000.vcf 0001.vcf 0002.vcf 0003.vcf README.txt sites.txt Where the README.txt says: dir/0000.vcf for stripped <file1.vcf.gz> dir/0001.vcf for stripped <file2.vcf.gz> dir/0002.vcf for stripped <file3.vcf.gz> dir/0003.vcf […]

install ensembl-vep 0 Hello, I want to install ensembl-vep in my Ubuntu 18.04.2. I have already installed LWP::Simple. What can I do in the next step? Thanks in advance for great help! Best, Yue Inspiron-3670:~$ perl -MCPAN -e’install “LWP::Simple”‘ Reading ‘/home/jing/.cpan/Metadata’ Database was generated on Sat, 07 Aug 2021 06:55:53 GMT LWP::Simple is up to […]

Merge files in Plink 0 Welcome… I have Est1000HGDP data and this data is in a PLINK format: Est1000HGDP.bed Est1000HGDP.bim Est1000HGDP.fam I have other data from the study by Henn et al. 2012 in the same format: Henn.bed Henn.bim Henn.fam And I want to merge these files with each other, and unfortunately I tried many […]

How to get good mapping for miRNA-seq data by removing rRNA/tRNA 0 I have 50 miRNA-seq samples from mammary tissue of cow. my data had no linker and adaptor. After quality trimming I aligned the. samples with bovine reference genome Bowtie with following command: bowtie -m 10 -l 18 -n 1 -e 80 –best –strata […]

How to separate sub-families from transposons sequence based fasta files? 1 I’m working on the classification of transposable elements. I want to retrieve sequences of their sub-classes in separate files. Is there any code or tool present to separate their sub-families because dataset contains thousands of sequence entries for different species. I really appreciate any […]

Aug. 7—A Maryland woman died Friday while hiking in Maine’s western mountains. Barbara Goldberg, 78, of Potomac, Maryland, was dropped off about 9 a.m. in Stow, where she intended to hike Blueberry Mountain, according to Mark Latti, a spokesperson for the Maine Department of Inland Fisheries and Wildlife. Her partner, Steven Plotkin, talked to Goldberg […]