Community Digest

Top new questions this week:

Does cutadapt trim trailing N's first and then use max_n to filter reads?

Background I want to trim leading and (likely just) trailing N's from my WES (Illumina NextSeq500) reads with cutadapt (--trim-n)...

quality-control trimming cutadapt  
user avatar asked by Eva Score of 3
user avatar answered by Jesse Score of 3

How to improve this WGCNA analysis

This is my first time working on using WGCNA on a microarray dataset. One of the major problems I am facing is merging close modules which is not really working well. I have quantile normalised the ...

wgcna  
user avatar asked by siddhartha das Score of 3
user avatar answered by Peter Langfelder Score of 3

Writing to .cif from BioPandas

My question is twofold. First, I've run into an issue working with .cif files and pandas dataframes. With BioPandas, I can read a .pdb file into a dataframe and then go the opposite direction, writing ...

python biopython protein-structure structural-biology  
user avatar asked by Brookspj Score of 2

How to get started with louvain/leiden algorithm with UMAP in R

A collegue of mine recently suggested to try the louvain algorithm for clustering multiplex cytometry data. However, implementations of louvain are kind of rare in R. To my knowledge the only stand-...

r seurat clustering umap  
user avatar asked by r-newbie Score of 1
user avatar answered by M__ Score of 0

pip installation within conda env: Error downgrading scikit-learn - WARNING: No metadata

I am trying to get the bioinformatics tool deepbgc up and running. Now I have created a conda environment and have currently ...

python deeptools conda scipy pip  
user avatar asked by Joe_G Score of 1
user avatar answered by M__ Score of 0

Identifying highly variable genes in scRNA-seq: Seurat vs M3Drop

Following a single-cell RNA-seq workshop, I created a Seurat object (my_data), normalized the data, and then tried to identify highly variable genes using two ...

seurat single-cell  
user avatar asked by Judit Score of 1

Nested variable expansion in WDL code block

I am developing a gatk pipeline for variant calling and want to include trimmomatic as a preprocessing step. I would like the user to specify a program file of parameters to feed into trimmomatic, and ...

wdl  
user avatar asked by user16196 Score of 1

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  
user avatar asked by llrs Score of 14
user avatar answered by Kamil S Jaron Score of 4

How can I calculate gene_length for RPKM calculation from counts data?

I have read counts data and I want to convert them into RPKM values. For this conversion I need the gene length. Does the gene length need to be calculated based on the sum of coding exonic lengths? ...

gene gtf gencode fpkm  
user avatar asked by stack_learner Score of 11

How do I find identical sequences in a FASTA file?

I want to create a database for a proteomics study. Therefore, the mapping from a given sequence to a protein ID has to be unique. I am wondering whether there is already a built-in function in ...

python fasta biopython filtering  
user avatar asked by Cleb Score of 10
user avatar answered by Bioathlete Score of 8

Calculating average coverage for .bam files (sequence data)

(Full discolosure that this is my first time working with sequence data, and with the bash scripting.) I need to calculate the average coverage for any .bam file. After some searching I wrote the ...

sequence-analysis bash coverage  
user avatar asked by Mirte Score of 4
user avatar answered by Konrad Rudolph Score of 8

Obtaining uniquely mapped reads from BWA mem alignment

This is based on a question from betsy.s.collins on BioStars. The original post can be found here. Does anyone have any suggestions for other tags or filtering steps on BWA-generated BAM files that ...

bam alignment bwa  
user avatar asked by gringer Score of 19
user avatar answered by gringer Score of 13

Why Ti/Tv ratio?

I'm interested in the transition/transversion (Ti/Tv) ratio: In substitution mutations, transitions are defined as the interchange of the purine-based A↔G or pryimidine-based C↔T. Transversions are ...

variant-calling  
user avatar asked by SmallChess Score of 9
user avatar answered by user172818 Score of 8

What is the index fastq file (sample_I*.fastq.gz) generated when demultiplexing Illumina paired-end runs?

What is the index fastq file that comes with some Illumina sequencing datasets? (The samplename_I*.fastq.gz file.) For example, I recently received some 10X ...

sequencing illumina 10x-genomics demultiplexing  
user avatar asked by conchoecia Score of 10
user avatar answered by conchoecia Score of 9
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