Community Digest

Top new questions this week:

Unexpected error using "stdin" in bedtools intersect as a piped command

From the bedtools intersect man (for version 2.30.0): ...

asked by Jeff 1 vote
answered by ATpoint 2 votes

splitCsv map with text, join with another channel, nextflow

I have a csv file which describes number of chunks per chromosome, like; ...

asked by zillur rahman 1 vote

Use conditional in workflow in Nextflow dsl2

How should I do: ... if ($(params.aligner) == "bowtie") { align_bowtie2(get_fq_info.out.fq_info) } else { align_bwa(get_fq_info.out.fq_info) } ... ...

asked by aerijman 1 vote
answered by Steve 1 vote

Timeout when downloading the ncbi nr blast database

I am experiencing timeout problems when downloading the NCBI nr preformatted blast database using the update_blastdb script (version 504861). I run the script with the following paramters ...

blast ncbi  
asked by C. Zeil 1 vote
answered by Life_Searching_Steps 0 votes

Nextflow: Can I parameterize similar processes inside a for loop?

I have set of ~5 processes which perform very similar tasks such that their differences can be parameterized. Rather than putting 5 items through some channel (which seems complicated), or defining 5 ...

asked by Brendan Hill 1 vote
answered by Pallie 1 vote

Greatest hits from previous weeks:

What Ensembl genome version should I use for alignments? (e.g. toplevel.fa vs. primary_assembly.fa)

When you look at all the genome files available from Ensembl. You are presented with a bunch of options. Which one is the best to use/download? You have a combination of choices. First part options: ...

fasta genome ensembl biomart  
asked by story 20 votes
answered by Devon Ryan 12 votes

Understanding DESeq2 design, contrast and results

I have a set of high-troughput experiments with 2 genotypes ("WT" and "prg1") and 3 treatments ("RT", "HS30" and "HS30RT120"), and there are 2 ...

r bioconductor deseq2 differential-expression  
asked by bli 17 votes
answered by bli 8 votes

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. ...

asked by novicebioinforesearcher 11 votes
answered by Devon Ryan 10 votes

RNAseq: Z score, Intensity, and Resources

I'm very new to bioinformatics in general, and I'm trying to understand some basic concepts. I have RNAseq data, and bioinformatics people tell me that intensities cannot be compared across patients. ...

rna-seq bioconductor python normalization  
asked by julianstanley 4 votes
answered by benn 3 votes

Are mitochondrial genes to exclude in scRNA-seq such as ribosomal genes?

In this answer, it is stated that ribosomal genes should be excluded prior to normalization in scRNA-seq as contaminants. Do mitochondrial genes have to be excluded as well? I plotted the top 50 ...

rna-seq scrnaseq quality-control  
asked by gc5 8 votes
answered by gc5 6 votes

Manually define clusters in Seurat and determine marker genes

I want to define two clusters of cells in my dataset and find marker genes that are specific to one and the other. Is there a way to do this in Seurat? Say, if I ...

r single-cell seurat  
asked by Nikita Vlasenko 5 votes
answered by plat 3 votes

How can longest isoforms (per gene) be extracted from a FASTA file?

Is there a convenient way to extract the longest isoforms from a transcriptome fasta file? I had found some scripts on biostars but none are functional and I'm having difficulty getting them to work. ...

fasta isoform filtering  
asked by ZincFingers 9 votes
answered by Devon Ryan 5 votes
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