How to use Homer for ChipSeq annotation??

I have called peak with MACS2 and trying to annotate with Homer but its not considering Hg19 and output comes as NA NA ....is there any one who can help me to use Homer for Annotation. I used...

07 August 2019 5,986 1 View

Can any one help me to get Agilent sure select Exome .bed file?

I want to do some comparison hence required Agilent sure select Exome .bed file?

08 September 2018 4,148 0 View

How to convert GFF file to GTF or GFF3?

i have gff file i can convert it too .bed file but i dnt kno how to convert it to gff3 or gtf please inform me if there is any tool for conversion. thanks

09 October 2014 5,427 0 View

How to identify gene location and annotation for noval genome??

I would like to know which software can provide annotation of gene and its location in noval genome

08 September 2014 6,604 9 View

Does anyone have experience with Primer designing via MagicViewer for SNPs generate only input and output file dint get final .exl file?

07 August 2014 301 0 View

How can one reduce the number of primers predicted by PrimerPro?

06 July 2014 5,354 2 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody....

01 March 2021 3,607 3 View

Genome-wide gene identification protocol ?

Is there any book chapter/book, webpage or research article available to understand genome-wide gene identification?

28 February 2021 8,095 1 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

Any specific pipeline or parameter to analyse total transcriptomics study of brain tissue samples?

I have two groups of brain samples, control and treated for example. It was total RNA nova seq sequencing. I tried all the available pipeline like: star+rsem+deseq2, Hista+stringtie+cuffdiff,...

27 February 2021 356 6 View

Runs of nucleotides in Sanger sequencing?

I performed site directed mutagenesis, transformation, and then I sent out plasmids for Sanger sequencing and found out that there is extension of DNA just before the stop codon. I am not sure...

27 February 2021 547 3 View

Has anyone used the Illumina ITS1 primer sets?

Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...

25 February 2021 6,969 3 View

How do I choose contrasts in SPM8?

I am learning how to use SPM for PET and PET-MR analysis, but I haven't found any great resources that explain how contrasts work. I have a series of PET images where our hypothesis argues that...

24 February 2021 1,534 2 View

Errors in DNA sequences?

I am trying to better understand the scope of DNA replication and sequencing errors, e.g. 1. I have seen similar error rates of 10e4 to 10e5 for cell & instrumental DNA replication,...

24 February 2021 4,397 3 View

RNA-seq DEGs downstream analysis and reporting in literature?

I used EdgeR to get the list of DEGs (differentially expressed genes) from my liver RNA-seq experiment. I have done the gene overrepresentation and GSEA based pathway analysis. I am currently...

23 February 2021 8,969 1 View