Community Digest

Top new questions this week:

why in RNA seq don't we only use reference transcriptome?

I would like to ask why in RNA seq analysis (alignment step) we use sometimes reference genome instead of reference transcriptome? thank you!

rna-seq alignment  
asked by marilu 1 vote
answered by swbarnes2 5 votes

Power calculation for GWAS/EWAS

I want to investigate, how much sample size i needed to obtain 80% power for GWAS/EWAS studies. Phynotype trait is discrete (not case/control) for human disease. I wonder, does anyone has came across ...

bioconductor gwas human-genome population-genetics molecular-genetics  
asked by user2808642 1 vote
answered by Michael 1 vote

What is a good rule of thumb for the threshold of noise versus signal for RPK in RNA seq?

I have RPK values (RNA seq) and I'm wondering what is a good rule of thumb for what is considered to be noise versus what is considered to be signal? I.e what should I choose as a threshold value for ...

rna-seq normalization  
asked by An Ignorant Wanderer 1 vote

Modifying protein_scale in ProteinAnalysis in SeqUtil in Biopython?

Is there a way to give weight arguments to each of the residues when using protein_scale in the ProteinAnalysis module of Bio.SeqUtils.ProtParam? I thought this would be done with the window and edge ...

proteins biopython  
asked by mzzx 1 vote
answered by Matteo Ferla 3 votes

What are the symbols of $*$ and '$\_$' in an unknown alignment format for HLA data from the IMGT dataset?

Has anyone worked with the IMGT HLA database/dataset before? IMGT-HLA git repo they have some convenient text files (eg. link to gene A .txt file) with the genomic data for the different alleles of ...

sequence-alignment alignment  
asked by Vass 1 vote

What is the best approach to classify a patient cohort by the expression (low, int, high) of a single gene of interest?

I am working with a dataset of nearly 100 patients. I performed Salmon quantification with genecodeV34 and imported the results with tximeta. I normalised the TPM salmon output with TPM (using edgeR, ...

rna-seq gene-expression clustering  
asked by FrAoJm 1 vote

Find all the bases for given reference position

Hi im looking for the aligned bases in the reads for a given reference position. im using the following script from the pysam documentataion. I adjusted it to find the specified position. in this case ...

sam pysam  
asked by Diesel__100 1 vote

Greatest hits from previous weeks:

How to convert fasta file to tab delimited file

I have a fasta file like >sample 1 gene 1 atgc >sample 1 gene 2 atgc >sample 2 gene 1 atgc I want to get the following output, with one break between the header and the sequence. ...

fasta format-conversion  
asked by AudileF 11 votes
answered by terdon 11 votes

Converting a VCF into a FASTA given a reference with Python, R

I am interested in converting a VCF file into a FASTA file given a reference sequence with Python or R. Samtools/BCFtools (Heng Li) provides a Perl script vcfutils.pl which does this, the function ...

r python fasta vcf samtools  
asked by ShanZhengYang 10 votes
answered by Jared Andrews 5 votes

What is a quick way to find the reverse complement in bash

I have a DNA sequence of which I would like to quickly find the reverse complement. Is there a quick way of doing this on the bash command line using only GNU tools?

sequence-analysis dna bash  
asked by winni2k 5 votes
answered by winni2k 13 votes

Difference between samtools mark duplicates and samtools remove duplicates?

What is difference between samtools mark duplicates and remove duplicates ? Is it necessary to mark duplicates before removing duplicates with samtools?

alignment ngs samtools  
asked by Ammar Sabir Cheema 5 votes
answered by Kohl Kinning 3 votes

Converting Gene Symbol to Ensembl ID in R

I'm trying to convert ~20,000 different human gene symbols to ensembl IDs. I've been trying to use biomaRt to do this, but continue getting the following error getBM( attributes=c("ensembl_gene_id") ...

r gene ensembl biomart  
asked by Mea R. 3 votes
answered by llrs 7 votes

Read length distribution from FASTA file

I have a ~10GB FASTA file generated from an Oxford Nanopore Technologies' MinION run. How can I quickly and efficiently calculate the distribution of read lengths? A naive approach would be to read ...

fasta nanopore  
asked by Scott Gigante 23 votes
answered by Sam Nicholls 16 votes

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 ...

software-development publishing  
asked by Tom Kelly 12 votes
answered by Devon Ryan 12 votes
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