2bwt-build fialed for big data, how to deal with TextLengthFromBytePacked > 2^32?

When I used soap2 for performing alignment, the 2bwt-builder failed as my reference genome is too big. Does anyone know how to solve this problem? Thank you!

03 April 2018 8,128 0 View

Can any one help me with prediction.function based on distance matrix in R?

31 December 2015 4,618 2 View

How to convert solid csfasta to fasta file?

Does any know how to convert solid csfasta to fasta file? And is there any problems involved in it? Thank you! The csfasta data is something like this: >...

31 December 2014 4,374 0 View

How do you improve the bootstrap value in the phylogenetic tree in MEGA?

Any suggestion?

10 November 2014 5,567 7 View

No title

The link is right here :http://www.hmpdacc.org/doc/sops/reference_genomes/metrics/Bacterial_CoreGenes_SOP.pdf I do not understand some points in it clearly: If the query is the amino acid...

09 October 2014 3,190 1 View

Who's running quake?

how to deal with the error as below? Read 30000 itemsError in est.cov(cov) :Cannot identify reliable trusted k-mer coverage peak. Please verify the integrity of your dataset (e.g. by running...

08 September 2014 2,134 0 View

What is the difference between genotype and haplotype data in the ped format?

Hi everybody In the ped format for genotype, alleles of any SNP are represented by two columns (one for each allele, separated by a space). Is a column sufficient for the haplotype to...

27 February 2021 1,965 1 View

Are there any databases for gene co-expression or expression pattern clustering?

I am currently working on gene clustering based on co-expression pattern in mouse brain. The problem is I do not have some solid way to test my result. Are there any suggestions for databases...

22 February 2021 4,374 3 View

Useful architecture for bioinformatics?

Hi Dear researchers In ensemble-based architectural design Which algorithms are more useful for classification? What is the difference between parallel and ensemble architecture? Thanks I am...

08 February 2021 2,727 5 View

Electron density difference maps(Fo-Fc): what is the meaning of negative densities (red blobs)?

Dear community, As far as I understand, negative density features point at stuff that is in the model, but not supported by experimental data. However, in many cases (e.g. attached image), when...

06 February 2021 2,847 2 View

Is it possible estimating environmental conditions with a Bayesian approach?

In ecology specific species can be used to get an indication/estimation of the environmental conditions. A simplistic example, lets assume I find a pike (Esox lucius). We know this species does...

01 February 2021 10,034 4 View

Qiime2- No reads passed the filter. How to set the trunc value?

Hi, I am working on some 16S sequencing data, and seems some of them are low quality. I am not sure how to set the trunc value in dada2. qiime dada2 denoise-paired \ --i-demultiplexed-seqs...

30 January 2021 6,213 3 View

Which software to use to statistically analyze Telomere Length_TRF_Southern Blot?

I am trying to measure telomere length in an ant species using the TRF method, which is a Southern blot technique. Currently, I am struggling with analyzing the images and would appreciate any...

29 January 2021 604 3 View

MHC Rabbit Genome Annotation? Domain annotation of each MHC Rabbit Gene?

I want to find a database(s) or a method where I can find and bulk download all the rabbit MHC genes and domain annotation. In humans using Ensembl, all MHC genes have names and domains but in...

28 January 2021 7,722 2 View

What is the half-life of TNF-alpha in vitro?

I'm designing a low-grade chronic treatment with this cytokine and I'm wondering how regularly to change the culture medium based on the half-life of the protein in an in vitro environment....

24 January 2021 5,988 2 View

Best tool to build missing residues, minimize and validate a ligand model?

I am working on a ligand that is co-crystalized to parotein, but the ligand is missing some residues that makes it appear as if it was separated into two ligands! what I need is to connect them...

23 January 2021 3,975 7 View