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Homer findGenomeMotif.pl ghostscript error?

Hello everybody, I am running HOMER to find motif for my factor of interest. I should get motifs in many formats such as png, pdf and motif formats. unfortunately the script gives the following...

04 May 2015 2,599 6 View

Does anyone know a good efficient protocol to isolate nuclei from Drosophila larvae nuclei to be used later in native MNase-ChIP as well as 3C assay?

06 July 2014 252 4 View

How to draw nucleosomal array?

Does anyone suggest a program or tool to draw nucleosomal array? Thanks a lot!

03 April 2014 711 2 View

Does anyone have an idea how to use SILAC to test protein-protein interaction?

06 July 2013 8,966 1 View

Does anyone know how to design LNA attached with spacer sequence?

I want to design LNA for chromatin pulldown. Can any one help?

31 December 2012 7,266 1 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

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

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

If my gene of interest has high GC content can it be problematic in sequencing? What kind of error is expected with GC rich gene sequences??

Gene sequencing related trouble shooting

25 July 2024 4,149 2 View

Does post-translational protein modification cause devisions on observed pI verses calculated pI?

In running two-dimensional gel electrophoresis on bacterial protein, some spots that appear to match a protein sequence have a significantly more acidic isoelectric point than the calculated pI....

24 July 2024 8,076 3 View

Which software tools are best for enhancing diagnostic accuracy in chest X-ray imaging using image reconstruction and neural networks?

I am reaching out to seek your valuable advice and recommendations regarding the best software tools to use for this research. Specifically, I am looking for software with a user-friendly...

22 July 2024 3,794 1 View

Are there always been barcodes, apapters and primer sequences in the FASTQ files of NGS?

Hello researchers, Sorry for my stupid question. I am learning the QIIME2 workflow for analyzing some 16s amplicon NGS fastq data. I found a very nice paper with data and code public available...

20 July 2024 5,405 2 View

I want to conduct a research using quasi experimental design to test two treatment and one control what type of statistical tools do l use ?

What type of experimental design do l use and what statistical tools do l use for the hypothesis. What is the position of control group in the analysis?. Thanks

18 July 2024 3,581 3 View

Promotor observation in region annotation of RNA RIP-seq?

Hello all, I extracted RNA from my samples and performed RIP-seq. After annotating the genomic regions using R, I obtained promoters, exons, introns, and UTRs. Given that my samples consist of...

18 July 2024 1,579 2 View