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How to create a nexus file for BEAST?

I am learning to use BEAUTI and BEAST software. I followed their tutorial and was able to run example data without any problem. Now, I want to do phylodynamic analysis on my data. I have downloaded 70 picornavirus sequences from the gene bank. My…
L R Joshi
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How to extract the protein fasta file from a genbank file?

Let's say I have a genbank file, e.g. the one downloaded from here, that contains entries as gene 190..255 /gene="thrL" /locus_tag="b0001" /gene_synonym="ECK0001; JW4367" …
Cleb
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RunUMAP in Seurat not working: module 'umap' has no attribute 'UMAP'

I am trying to run UMAP in the following way: RunUMAP(seurat_object, dims.use = 1:15, reduction.use = "pca", reduction.name = "umap", reduction.key = "UMAP", n_neighbors = 30L, min_dist = 0.3, metric = "correlation") Or just…
Nikita Vlasenko
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How to apply function on bedfile based on a reference bedfile

I have two bed-like files: File1 chr1 1 10 . 1 Sample1 chr1 20 180 . 1 Sample1 chr1 1 5 . 1 Sample2 chr1 70 100 . 1 Sample3 File2 (reference) chr1 1 5 . 0 chr1 5 …
gc5
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How can I get a list of papers where a particular mutation has been mentioned?

I have recently tried a few tools (MutationFinder, tmVar, PubTator etc.) that extract mutations from a given text. However, for my work I need something that will take a list of mutations as an input and return a list of pubmed id in which the…
Musfiqur Rahman
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3 answers

Is there a way to do GWAS on phenotype data that is not normally distributed?

Is there a way to do GWAS on phenotype data that is not normally distributed? For example, if you were measuring a trait as a proportion, and the majority of the data consisted of 0.00 with a long tail of variation. Or, perhaps the data was skewed…
jhurst5
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How to extract exome on-target reads in batch?

I was given a list of target regions in BED and many exome alignments in BAM. I was asked to extract on-target alignments from these BAMs to save disk space. I know I can use bedtools to extract sub-BAMs. I am thinking to write a script to apply…
medbe
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1 answer

BioMart Ensembl id imperfect retrieval

I have a list of gene symbols: c("cd45", "Tmem119", "CD11b", "P2Yr12", "Csf1r", "Bst2", "Cd74", "Cx3cr1", "Trem2", "Lyz2", "GLAST", "GFAP", "ALDH1L1", "Aldoc", "Aqp4", "Glul", "S100a", "Olig1", "Olig2", "Olig3", "Mbp", "Pdgfra", "Pecam", "Cldn5",…
Nikita Vlasenko
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1 answer

tximport txidcol and geneidcol selecting wrong column

I'm trying to run a differential expression analysis of 2 samples of the same species, but with different treatments using DESeq2. I'm using Ensembldb to create a tx2gene dataframe for tximport, however tximport does not select the columns I…
wolff
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Will blastn remove sequences from a search with low identity?

I'm using this command (excuse the duplicate naming, I know it's bad form): blastn -query cm-seqs/combined_seqs.fna -db combined_seqs.fna -out cm-matched.txt -num_alignments 1 -outfmt 10 to take a set of fasta sequences to blast against another…
Samaj Oruel
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1 answer

What are negative FSC-A values in flow cytometry data?

I did flow cytometry analysis of E. coli cells 7 hours post inoculation (1% overnight culture in 3ml). I am analysing the FCS3.0 files using the flowCore package in R. I observe that FSC-A has negative values in some events, although the…
WYSIWYG
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Official documentation for textual BLAST output?

This is pretty vexing: I got asked to explain the meaning of the match line in a blastp output, especially the subtle difference between a blank and plus. E.g.: Query 181 NHIEEL... N I+EL... Sbjct 181 NQIKEL... For me this is…
BaCh
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How can I find the chromosomal location of a list of genes?

I have a list of genes nearly 20000: gene name (column1) and coordinates (columns 2 and 3) head genes Ma0_73Ns 2359 2923 Ma0_73Ns 4727 4868 I want to find the chromosomal location of each gene, on which…
Anna1364
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Is there a publicly available tumor-normal sample?

I am looking for a publicly available matched tumor-normal sample. I need Illumina fastq reads (or an aligned bam file, since I could extract the reads from it) from a tumor and a matching, non-tumor control set from the same patient. Ideally, I…
terdon
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2 answers

Generate SNP/indel annotation in Arabidopsis

I have a genome-wide list of germline SNPs and short indels for Arabidopsis thaliana, which I generated with Varscan. Regardless of the tool used to generate them, I would like to annotate them, i.e. knowing which ones can cause an aminoacid change…
Federico Giorgi
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