Hello! I am trying to analyze some RNAseq data I recently received. I would like to craft a heatmap comparing the expression of specific genes across my cell samples, but I am not sure which of the apps to use?
I have a dataset with about 80 different species. As usual, some species are very easy to identify with certainty whereas others are more difficult, which means that I am less certain of my...
03 March 2021 8,066 4 View
I have prepared a manuscript in IEEE Latex template, but for some purpose, I need to prepare a word file as well (detailed format is not required). Compared to two column .tex file, one column...
02 March 2021 1,830 3 View
Gel electrophoresis, RNA degradation, RNA extraction from fresh tissue
02 March 2021 5,433 5 View
Hello, I would like to ask how to grow E.coli which resists 50 or 100ug/ml of Blasticidin. I have tried many methods by using low salt Luria-Bertain(LB) agar plate. However, no colonies grow. Let...
01 March 2021 2,027 2 View
I'm looking to try out an off-the-shelf EEG set for some exploratory work. Curious if anyone has used the OpenBCI, and how much set-up work is required. I've heard they are more difficult to get...
01 March 2021 4,128 3 View
I am doing a acid and a chiral amino alcohol reaction using DCC and HOBT in DCM or THF? Can anyone suggest me how to remove DCU and HOBT from a reaction mixture??
28 February 2021 2,153 1 View
Favourable conditions of base pressure, rate of deposition. Also, by which characterisation technique to be used to verify the thickness of the deposited film.
28 February 2021 3,640 3 View
The following code (see 1st 2 images attached) is used to produce PID controller values that are designed to control the system (G). The code finds the PID controller values (noted as k) by using...
28 February 2021 6,560 14 View
Hi everybody, I have been running a multiplex IHC which allow me to stain the same tissue with different markers (Primary Ab + Secondary conjugated Ab) (AF487, AF555, AF647). Since I would like to...
27 February 2021 5,028 2 View
What is the disadvantages of high sulfur content to the ceramic burning process? and what is the effect of outranged viscosity?
24 February 2021 8,219 2 View
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
Hello, I have demultiplexed my short reads and I have removed the Illumina adapter left in the sequences and now I need to remove the barcodes used by the sequencing centre from my reads. I have...
22 February 2021 9,873 3 View
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
Genotyping data is from Illumina Global screening array 24 v 2.0 and ConsistencyDupSNP.sh file contains list of pair of duplicated SNPs in GSA24 v 2.0.
18 December 2020 1,966 3 View
I am interested in the different tools that can be used to create custom databases for targeted sequencing and how to trim the databases based on the amplicon size? Also, should custom databases...
02 December 2020 3,105 3 View
I am looking to run illumina miseq data through dada2, but the limited identification of this gene means there are no pre-build databases. I have a database built in MOTHUR format, does anyone...
30 November 2020 8,228 3 View
I downloaded the expression matrix data "GSE143416_Brain_data_TPM.txt.gz" of GSE143416 from Gene expression omnibus ( https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi). However, the first column of...
30 November 2020 1,304 3 View
Adding heterogeneity spacers to primers used for Illumina based amplicon studies has proven to improve read quality by increasing bp diversity on the flow cell during sequencing. I have seen two...
01 November 2020 9,071 3 View
I am looking for opinions/recommendations of NGS Platforms (Illumina vs. BGI/MGI) from people that had opportunity to work on both hardware: MGISEQ-T7 and NovaSeq 6000 or analyze data from both....
04 October 2020 8,125 1 View
I recently performed plasmid extraction and nanopore sequencing. I have found what looks like a plasmid with replicon types IncX and IncF. Even with spAdes, canu, unicycler (illumina and nanopore...
29 September 2020 7,778 2 View