ExPecto

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Could expecto accepts fasta input and return the prdicted tissue-specific expression values?

2

Hi, thanks for the great tool! I notice that expecto takes a sequence around TSS to predict the tissue-specific expression values and calculate the expression difference between ref and alt...

WeiCSong

Sequences < 1,000bp

9

How does Beluga handle sequences < 1,000bp? Does it center on the input sequence and pad it with N's, or does it do something else? Thanks!

imk1

How to repeat file Xreducedall.2002.npy for another organisms

4

Hi， Could you provide the python script to produce Xreducedall.2002.npy file, pls? Maybe we can use the pipeline for another organisms analysis, such as FLY. Thansk in advance!!! Best Wishes,

Jasonxu0109

averaging forward and reverse strand from output of chromatin.py

2

For other purposes I wanted to get a single chromatin effect score for each SNP from what I can tell if X = num_variants then for each SNP i then...

cmlakhan

The representative TSS site

1

I'm interested in the method to get the representative TSS site you provided in "Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk". In the...

ivyhzau

difference of the result between predict.py and website (HumanBase)

1

Hi, I used the script "predict.py" to do the prediction of a vcf file, and I find that there is some difference between these results and the results from ExPecto...

zofieLin

About the download of 2002 feature files

6

Hi, I want to get 2002 narrow-peak files of matin features, but I did not provide the link in the file "deepsea_beluga_2002_features.tsv". I can only download 874 of them through...

Licko0909

I am running this program on a shared cluster and using data for ~1,000 variant mutations worked within the constraints of system/memory usage for jobs on this cluster; however, trying...

washedgram

Replicating features in resources/Xreducedall.2002.npy

2

Hello, I'm trying to replicate the features in `resources/Xreducedall.2002.npy`. I am able to get within 99% spearman correlation, but I'm not able to replicate the features exactly. Would you be...

AvantiShri

Discrepancy between architecture in paper and architecture in deepsea.beluga.2002.cpu

1

Thank you for making your code and model available! I just wanted to bring it to your attention that there appears to be a discrepancy between the architecture specified in...

AvantiShri