Top new questions this week:
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Background I want to trim leading and (likely just) trailing N's from my WES (Illumina NextSeq500) reads with cutadapt (--trim-n)...
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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 ...
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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 ...
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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-...
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I am trying to get the bioinformatics tool deepbgc up and running. Now I have created a conda environment and have currently ...
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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 ...
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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 ...
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Greatest hits from previous weeks:
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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 ...
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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? ...
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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 ...
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(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 ...
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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 ...
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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 ...
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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 ...
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