RNASeq How many reads do I need for RNASeq 19 Nov 2020 For gene expression profiling experiment: 20M reads, single-end (often 50–75 bp)Need to look at alternative splicing: 30-60M reads should aim for PE 2*75bp or 2*100bp also use with stranded RNA-Seq…
NGS Next-generation computational tools for interrogating cancer immunity | Nature Reviews Genetics 17 Sep 2019 The interactions between tumours and the immune system are highly complex. This article discusses methods — primarily computational tools — for characterizing diverse aspects of cancer–immune cell interactions, including antigen…
NGS Improving the quality of cancer tissues for research 25 Oct 201825 Oct 2018 Through careful characterization of specimens, a new study has come up with some conclusion on how we can improve the quality of cancer specimens for research. Read the summary on…
genetics… Using public exome database as your control in WES association studies 17 Oct 201817 Oct 2018 Checkout the new software release TRAPD, which stands for (Test Rare vAriants with Public Data) https://github.com/mhguo1/TRAPD Read the detail on the article published in AJHG this month at https://www.cell.com/ajhg/fulltext/S0002-9297(18)30284-2
NGS A note on getting start with samtools on Mac OsX 10.8.5 Mountain Lion 20 Feb 2014 samtools is a handy tool for sequence alignment and mapping (http://samtools.sourceforge.net/ For more information, please refer to the original article here: Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan…
bash… How to wget with proxy authentication? 26 Jul 20132 Jul 2014 Once again, I have a problem with proxy server authentication through my university network. Trying to install the new KGGSeq software to do next-generation sequencing data analysis. As a quick…
genetics… Ion Torrent PGM vs PacBio vs MiSeq 16 Jun 2013 "It's a lot cheaper to buy PGM compared to other sequencing platform. So, should we buy it?" A common concern regarding this question is whether the sequencing quality is alright?…