Bioinformatics Stack Exchange Community Digest

Top new questions this week:

Using SED command in Nextflow script

I was wondering if someone can help me figure out this error message. I’m at the end of my Nextflow pipeline and I want to change the header in a FASTA file and it works when I use this command: …

fasta nextflow errors command-line sed

asked by rimo Score of 3 answered by Steve Score of 4

Filter with bcftools

I want to filter a SNP, specifically CHROM1:POS:630128. I tried to use bcftools for this. I came up with the following variant …

vcf filtering bcftools

asked by mugdi Score of 2 answered by terdon Score of 1

Can I discard missing alleles?

I am converting a biallelic VCF into a SQL table and one of my tables will be something like: …

vcf genomics bcftools

asked by glycoaddict Score of 2 answered by JRodrigoF Score of 1

Removing particular line along with Fasta header in fasta file

I have a fasta file of 3’UTR sequences of the genes. Some of the gene do not have a 3’UTR sequence and reported with sequence unavailable but there is FASTA header. …

fasta awk grep

asked by Dr Sud Score of 2 answered by gringer Score of 3

Non-parametric, background-based tests on proteomics data from Proteome Discoverer v2.5?

I am new to proteomics analysis, so apologies if my question is silly! For context, I am working with proteome samples from the postmortem human brain for a case-control study. Our lab generally …

proteins statistics differential-expression proteomics data-preprocessing

asked by Kelly Score of 2 answered by xz99890 Score of 1

What are the columns in bedtools coverage output hist file?

I am using bedtools to caculate the coverage of my targets of my WES data, to later plot. But to plot, I need to know what to plot and what it is I am seeing. I have unsuccefully tried to find what …

sequence-analysis bedtools coverage exome

asked by Eva Score of 1 answered by Eva Score of 1

Only the first file Pair is processed from Channel.fromFilePairs()

This is my first nextflow pipeline and i am struggling with the .fromFilePairs concept of Nextflow. I want to process paired-end read files and align them against a reference genome. I use Hisat2 so …

nextflow rna-alignment

asked by stfn.snk Score of 1 answered by Steve Score of 0

Greatest hits from previous weeks:

Difference between CPM and TPM and which one for downstream analysis?

What the difference between TPM and CPM when dealing with RNA seq data? What metrics would you use if you have to perform some down stream analysis other than Differential expression for eg. …

rna-seq

asked by novicebioinforesearcher Score of 15 answered by Devon Ryan Score of 12

Fast way to count number of reads and number of bases in a fastq file?

I am looking for a tool, preferably written in C or C++, that can quickly and efficiently count the number of reads and the number of bases in a compressed fastq file. I am currently doing this using <...

ngs fastq software-recommendation benchmarking

asked by terdon Score of 12 answered by sjcockell Score of 14

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

asked by stack_learner Score of 11 answered by Devon Ryan Score of 7

Interpretation of the violin plots from sc-RNA-seq

I’m confused about the meaning of the black dots and the red shape in the violin plots from the seurat tutorial:

scrnaseq

asked by hua Score of 2

Download multiple SRA files

I want to download all SRA file from the following project. Is there a method to download all the SRA files at the same time?

rna-seq data-download

asked by user2300940 Score of 6 answered by benn Score of 4

Can open-source software be peer-reviewed and published?

My colleague and I have developed a software tool intend to release it open-source. This tool is specifically for tasks in bioinformatics but we think it would be helpful for the wider community. Our …

publishing

asked by Tom Kelly Score of 13 answered by Devon Ryan Score of 13

How to convert FASTA to BED

I have a FASTA file: …

fasta bed file-formats format-conversion

asked by SmallChess Score of 19 answered by SmallChess Score of 5

Can you answer these questions?

What does the “filters” argument in “getBM” do?

In the biomaRt package, there is a function getBM which among a few things is useful for mapping between different gene …

ensembl biomart

asked by An Ignorant Wanderer Score of 1

Calculating the correlation between GEX and protein

trying to calculate the agreement between the transcript – gene1 and the protein – protein1. I have the GEX data stored in “RNA” and …

r scrnaseq seurat gene-expression

asked by mmpp Score of 1 answered by gringer Score of 0

Why do I have missing values returned from getBM when converting Ensembl transcript IDs to gene names?

When I run the following R code to convert Ensembl transcript IDs to gene names and Ensembl gene IDs: …

r ensembl biomart

asked by An Ignorant Wanderer Score of 1