How to convert FASTQ to csFASTA and QUAL ?

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What is the best way to make an in-house database with allele frequency ?

Hi, I am currently working on making a variants database. I generate seperate VCF files for each samples them and merge them using VCFtools (using mergeVCF command) to make a multisample VCF...

31 December 2017 8,314 6 View

Sambamba-sort problem (not enough data in stream) ?

Hello, I'm getting an error: "sambamba-view: not enough data in stream" by running sambamba-sort, below my script : PS: I get this error only for some bam files but for all !! "sambamba view -t...

01 February 2017 5,139 0 View

How to create a test predictor with the genotype case/control study (genetic association) ?

Hello,I have a Case / Control genotype study (one qualitative phenotype). so I carried a genetic association analysis with PLINK (logistic) and I've identified hundreds of SNPs with very low Pval...

07 August 2016 1,507 4 View

How to calculate Gene-Gene Pearson correlation ?

I am stuck with a very simple problem. I want to build a Pearson correlation matrix for my RNA-seq dataset. My data file consists of normalized, log-transformed expression values of 60k...

31 December 2015 7,179 13 View

What option do you usually use with featureCounts to have count according to isoform ?

I am somewhat new to RNAseq data and I have been using featureCounts from the subread package to summarize reads/fragments across genomic features (genes, transcripts). In particular I am...

09 October 2015 5,126 1 View

How can I make a Polytomous analysis to define clusters in RNA-seq count data?

Hello, I have a RNA-seq count Data, with several conditions. and I'd like to do to a polytomous analysis to find the different clusters and their respective gene signatures. I find le package in R...

03 April 2015 5,453 3 View

How can I calculate the average values in dataframe with R?

I have a dataframe with a first column contains the gene symbol and the others column contains an expression values. the Column of symbol can contain the same symbol more then one time. So I would...

02 March 2015 2,107 5 View

How can I do clustering with RNA-Seq data ?

I have Cuffdiff (--no-diff) output tables and I want to perform clustering : 1) better to use Count or FPKM ? 2) Are "standard" clustering algorithms appropriate for RNA-Seq data due to its...

02 March 2015 7,802 23 View

Does anyone know how to estimate the inflection point using r?

How can I get the inflection point using r ?

01 February 2015 6,581 5 View

Is there a tool for converting a variable step wig to a fixed step wig?

Is there a tool for converting a variable step wig to a fixed step wig? Thank you in advance for your help

01 February 2015 1,030 5 View

Can I base on reverse DNA sequences to perform alignment, convert to amino acids and GenBank submission?

I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?

11 August 2024 5,138 1 View

How to confirm the site-directed mutagenesis result without performing NGS?

I'm cloning a fragment of 3200 nts into plasmid. The cloning was successful, however, 02 amino acids were mutated. Now I want to fix these 02 aa by site-directed mutagenesis technique using...

08 August 2024 4,645 2 View

GC-MS retention index prediticon?

Hello experts, Does anyone know any free software about retention index prediction ?

08 August 2024 7,403 2 View

Why did the authors extrapolate a phenotype that they experimentally proved in one bacterial strain across the whole genus of the organism?

I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...

05 August 2024 6,787 4 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

Does anyone have issues using Prepman Ultra reagent for MicroSeq ID bacterial, fungal and yeast sample preparation?

I have been attempting to extract DNA from Bacterial, Fungal and Yeast banked samples (>1e7 cells) using Prepman Ultra reagent and I seem to be struggling to obtain a sequence. Although the...

01 August 2024 2,079 0 View

Seeking Software Recommendations for SELEX NGS Data Analysis?

I am looking for software to help analyze SELEX NGS data, including alignment, sequence enrichment, and other related tasks. Can anyone recommend suitable tools or software? Best wishes, Waleed

30 July 2024 1,061 5 View

I am working on my Master's thesis on the biogeography of the genus Ruagea and I would like to ask, could someone help me to check whether my result?

I created a file with my outgroup and ingroup species using Beauti, ran it in BEAST, viewed it in Tracer, and then used TreeAnnotator to create a file that I imported into RASP. Could someone...

28 July 2024 2,979 1 View

Could you try using PeptiCloud and see if it's a useful tool for biology research?

PeptiCloud (www.pepticloud.com) is a bioinformatic platform that allows researchers to organize and share their data for their projects as well as collaborate with others in one place. Through...

28 July 2024 4,762 2 View

Should the amount of DNA input used for ChIP-seq library preparation be matched between the control and experimental groups?

Hi all. As a beginner in ChIP-seq experiments, I hope you understand that the following questions might be somewhat basic. I am planning to perform ChIP-seq or MeDIP-seq analysis to investigate...

28 July 2024 6,938 1 View