Questions tagged [encode]

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Help with running ATAC-seq using Encode pipeline

I am very new to ATAC-seq pipeline from Encode and trying to run on a HPC but not sure the steps after reading their instruction. https://github.com/ENCODE-DCC/atac-seq-pipeline Here is my json file: <...
Chris's user avatar
  • 101
1 vote
1 answer
691 views

tensorflow nn_model for DNA sequences: Matrix size-incompatible: In[0]: [2,1], In[1]: [784,300]

Hope anyone can help a beginner here. I'm building a proof-of concept tensorflow classifier for DNA sequences. However, the NN model does not let through train and test vectors saying the matrix size ...
monade's user avatar
  • 11
6 votes
1 answer
445 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 ...
xamax 's user avatar
  • 63
1 vote
2 answers
161 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 ...
Priya's user avatar
  • 351
5 votes
4 answers
276 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 ...
0x90's user avatar
  • 1,427
3 votes
1 answer
162 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/) ...
Ian Sudbery's user avatar
  • 3,321
3 votes
3 answers
269 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 ...
stack_learner's user avatar
7 votes
4 answers
496 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 ...
jaslibra's user avatar
  • 524
7 votes
2 answers
724 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 ...
juniper-'s user avatar
  • 890