sei-framework

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I wanted to train the Sei Model only on a subset of chromatin profiles than all 21907. I was wondering what needs to be changed to make that happen. I...

smasotti21

Error Kindly help

3

Hi, I ran the sh script like this `sh 1_sequence_prediction.sh /home/amit/Desktop/lingo1/regions/gain.HS.TEs.bed /home/amit/Desktop/lingo1/hg19/hg19.fa /home/amit/Desktop/lingo1/regions/TE_predict` 1_sequence_prediction.sh: 20: set: Illegal option -o pipefail Kindly help

amitpande74

Does reverse complement matter when using DNA sequence as input?

1

Hi, i'm wondering if it is neccessary to reverse all input DNA sequence to positive strand when using sei. Biologically speaking both strand should have the same peak but i'm...

WeiCSong

I’m currently working with the Sei model and I’m curious about the computational time required for it. Could anyone provide insights on how long it typically takes to compute outcomes...

liameihao

model training error

1

Command: python -u ./selene/selene_sdk/cli.py train.yml --lr=0.1 Error information: Traceback (most recent call last): File "train.py", line 11, in parse_configs_and_run(configs, lr=0.01) File "/home/user/.conda/envs/selene_sdk/lib/python3.7/site-packages/selene_sdk/utils/config_utils.py", line 344, in parse_configs_and_run execute(operations, configs, current_run_output_dir) File...

FarmOmics

will the trained model work for seq short than 4096

1

Hi, thanks for your great work! I am wondering whether you model will work for input sequence short than 4096 bp? I am trying to predict random sequence's expression activity...

jianglch

UnboundLocalError: local variable 'i' referenced before assignment

4

Hi, I was trying to predict the chromatin profiles by running `sh 1_sequence_prediction.sh $input_filepath $genome_version $outdir --cuda` but got the following errors. Can anyone helps for this? Thanks in advance....

ghm17

From seqclass score to seqclass prediction

3

Dear developers of sei, First, thank you for developing this amazing tool. I am doing variant effect prediction with sei and come up with this question. Apart from the seqclass...

JohnsonStev

CUDA out of memory.

1

Very good work. I'm using your data to train the model following your tutorials and I'm running out of memory on the GPU, how can I modify the train.yml file?...

tzhu-bio

Hi there, Thank you so much for making your research accessible! I wanted to ask a questions about the file`model/target.names`. Are these labels ordered in the same manner as the...

e-trop