Questions tagged [encode]

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Why does the ENCODE chip-seq pipeline discards reads with a hard-clipped alignment?

Hard-clipped alignments are alignments in which one or both the ends are clipped AND map to other genomic coordinates. As you may know, BWA-MEM reports hard-clipped alignments as supplementary. ENCODE'...
6
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1answer
312 views

Biohackers Netflix - DNA to binary and video

I'm not sponsored or anything, just interested in their challenge to decipher their DNA code. They encoded their first episode of "Biohackers" video/binary file to DNA code and said if we ...
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2answers
105 views

Transcription factor targets for Human and Mouse genes

I want to get transcription factor targets for my list of genes (For Human and Mouse) I have found ENCODE Transcription Factor Targets database (The link is given below). But I am looking for some ...
5
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4answers
199 views

How do you query and explore ENCODE data?

I am looking for a modular way to query data from ENCODE. For example, I would like to get CHiP-seq or similar tracks for a specific cell line. What's the proper way to do it? Finally, is there an ...
3
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1answer
112 views

Details of ENCODE processing pipelines

I am trying to find details for how the ENCODE ChIP seq samples were processed. Linking to a ChIPseq samples on www.encodeproject.org (e.g. https://www.encodeproject.org/experiments/ENCSR051DXE/) ...
2
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1answer
93 views

How to visualize genome track of gene in specific cell-lines?

I'm trying to make a plot showing genome tracks of specific genes in specific cell-lines of RNA-seq and Chip-seq data. It should look something like this I have recently seen this encode, but in ...
7
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4answers
219 views

Given a transcription factor, what genes does it regulate?

I have a list of transcription factors and I am interested in finding out which which genes might be transcribed as a result of the formation of transcription factor complexes with that transcription ...
7
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2answers
461 views

What is the difference between ENCODE Tier 1, 2 and 3 cell types?

The ENCODE Experiment Matrix at UCSC lists the different available cell types under the categories "Tier 1", "Tier 2" and "Tier 3". What is the difference between these classifications? What, for ...