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Old 04-03-2016, 02:14 AM   #1
ChengchenZhao
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Location: China

Join Date: Apr 2016
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Post Dr.seq: a quality control and analysis pipeline for droplet sequencing

Dr.seq is a QC and analysis pipeline for Drop-seq data.

Drop-seq is a powerful technology to analyze gene expression from thousands of individual cells simultaneously. It only requires 12 hours to prepare 10,000 single-cell libraries for sequencing (Macosko, et al., 2015; Klein, et al., 2015). The breakthrough of this technology provides many applications, such as the deconstruction of a cell population, the detection of rare cell types and the inference of interactions between genes.

Here we provided a powerful pipeline, Dr.seq, for QC and analysis of Drop-seq data.
With the help of Dr.seq, users can easily get through the basic analysis steps for RNAseq and our new developed analysis specifically for Drop-seq data, including STAMP selection(real cell selection, removing bias and empty barcodes), dimentional reduction(PCA & t-SNE) and cluster single cells to different groups (group number was automatically decided according to data preference).
Dr.seq is user friendly and DON'T have ANY requirements except basic Python and R.

We also provided a detailed "Quick Start" page for users to get familiar with Dr.seq within 3 steps ( on a linux/MacOS system with ONLY python and R installed.).

The latest version of Dr.seq software is available at bitbucket: https://bitbucket.org/Tarela/drseq.The related paper is accepted by Bioinformatics.

And the Quick Start toturial available here:
http://www.tongji.edu.cn/~zhanglab/drseq/index.html

By applying this pipeline, Dr.seq takes two sequencing files as input (data_1.fastq for barcode information, data_2.fastq for reads information, see our testing data and Manual section for more information) and provides four groups of QC measurements for given Drop-seq data, including reads level, bulk-cell level, individual-cell level and cell-clustering level QC.

I hope this proves useful to some people here. Any feedbacks will be appreciated.

Chengchen

Last edited by ChengchenZhao; 04-03-2016 at 04:21 AM. Reason: add details
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Old 08-22-2016, 07:12 AM   #2
hideandSEQ
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Location: New Haven

Join Date: Mar 2016
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Hi Chengchen,

I've been trying to check the program out but the only links on the pitbucket site are from the 1.1.2 version which doesn't seem to be able to install with python.

All of the links for the 1.1.3 version you released this year don't seem to work for me.
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Old 10-18-2016, 03:01 AM   #3
jspagnuo
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Location: Switzerland

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Thanks Chengchen,

Looking forward to using this in the near future!

Last edited by jspagnuo; 10-18-2016 at 03:06 AM. Reason: didnt RTFM
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drop-seq, pipeline development, quality control, rnaseq analysis, singe cell sequencing

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