Bioinformatics Stack Exchange Community Digest

Top new questions this week:

I need to index a GTF (gene transfer format) annotation file

This question was also asked on Biostars I created a GTF file for HLA alleles to be used as a resource for GATK Funcotator. Running Funcotator without indexing the GTF gives this error: ...

sequence-annotation gatk gtf indexing

asked by doodle Score of 3

answered by terdon Score of 1

PLINK to VCF seems to to not convert correctly, what am I missing

I have Illumina Infinium Global SNP array data that I want to compare to same sample WES data in VCF format. To do that, I am trying to convert the plink files (.bed, .bim and .fam) into vcf. I am ...

vcf snp variant-calling wes array

asked by Dandelion Score of 3

Samtools index fails within nextflow workflow but not outside of it

I am a beginner to Nextflow and using it to setup Chipseq workflow and in the workflow below the samtools_index process throws the following error: ...

nextflow

asked by siddhartha das Score of 1

answered by Steve Score of 2

Greatest hits from previous weeks:

What are the advantages and disadvantages between using KEGG or Reactome?

As enrichment analysis a usual step is to infer the pathways enriched in a list of genes. However I can't find a discussion about which database is better. Two of the most popular (in my particular ...

database

asked by llrs Score of 16

answered by Kamil S Jaron Score of 4

How to scale the size of heat map and row names font size?

I have an expression data matrix (120X15; 15 samples and 120 genes), my heatmap looks blurred and raw names (gene names) looks very small and can not read. How can I improve my scripts? Here is the ...

r rna-seq proteins clustering

asked by Kynda Score of 5

answered by sjcockell Score of 5

How to show bootstrap values on a phylogenetic tree constructed with RAxML

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 ...

phylogenetics phylogeny software-usage

asked by Leah Score of 2

answered by M__ Score of 3

Read length distribution from FASTA file

I have a single ~10GB FASTA file generated from an Oxford Nanopore Technologies' MinION run, with >1M reads of mean length ~8Kb. How can I quickly and efficiently calculate the distribution of read ...

fasta nanopore

asked by Scott Gigante Score of 28

answered by Sam Nicholls Score of 21

What do the read colors in IGV mean?

I was looking at a bam file in the IGV viewer and saw: What do the different read colors mean? Why is one read a light blue color, another green, another aquamarine (?), another purple and another ...

sequence-alignment visualization igv

asked by terdon Score of 5

answered by Ram RS Score of 5

Changing active.ident in Seurat

Im trying to change the active.ident to another column in metadata but this error keeps popping up! I recently upgraded to R version 4.0.2 from 3.6.1 The older version was working but the new one isn'...

r scrnaseq seurat sequence-annotation clustering

asked by Najeha Mohamed Score of 2

answered by haci Score of 2

changing color key range to specified range in heatmap.2 function

I have a tab separated text file as shown below ...

r bioconductor

asked by user3138373 Score of 4

answered by Devon Ryan Score of 4

Can you answer this question?

Approaches to add tracks / layers / grids to circlize::chordDiagram with specifications

I need to visualise additional information on my chord diagram made via circlize. I cannot figure out how to. I tried to highlight.section, but that did not seem to work as straightforward Let's use ...

r circos complexheatmap

asked by Joydeep Shaw Score of 2