Maisarah Ab Samad

7 Questions 2 Answers 0 Followers

Questions related from Maisarah Ab Samad

How to handle the 4 fastq files from one paired-end samples?

Hi. I received the fastq files for my ChIP-seq studies. We did 50 bp paired-end. I am new to the NGS. I used paired-end data from public files and usually, there were only two fastq files for...

14 July 2020 4,183 0 View

Samtools markdup for duplicate removal or Picard?

Hi everyone... I'm new in NGS analysis and I will work on Chip-seq and RNA-seq Im doing some analysis with published datasets I know this question is common in the NGS forums... When I search...

24 June 2020 6,138 2 View

Does preamplification affect the differential gene expression NGS analysis?

Hi, now I'm preparing library for SMART-seq2 using low input total RNA (~10 ng) The protocol i used is based on this paper: Picelli, S., Faridani, O. R., Bjorklund, A. K., Winberg, G., Sagasser,...

19 June 2020 8,558 0 View

Affordable machine for bioinformatics with minimum specs?

Hi, currently I'm searching for an affordable laptop with minimum specs for bioinformatics. My work will be NGS analysis (ChIP-seq & RNA-seq) I believe that MacBook is the best choice, but I...

02 June 2020 2,012 4 View

Why there is no significant entities after multiple testing (Benjamini-Hochberg FDR) in Agilent microarray data?

Hi. I have two conditions of my Gene Expression microarray data sets. The control/untreated and the treated sample. Each condition has two replicates. However, the first and second replicates...

06 August 2019 5,926 4 View

Does adding epitope tag in the middle of Homology arm and far from the DSB (~250 bp) is permissible for successful knock-in?

Hi. I want to knock-in 3xFlag-tag at the 3'end of my target gene, upstream of the stop codon. Hence, I will add the STOP codon after the 3xFlag-tag. Besides, I want to introduce...

19 October 2017 700 1 View

How can I troubleshoot when single digestion is not working?

Hi.. My vector is pGEM-T cloning vector (3kb) and my insert size is 1992 kb (~2kb). I use AgeI and KpnI for double digestion. For the competent cells, i use DH5a to clone the plasmid. I did...

13 June 2015 9,515 3 View