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expanded the first apperange of abbreveation; small grammar fixes
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Kamil S Jaron
Kamil S Jaron
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I guess, you're right that you need predictions of TFBStranscription factor binding site (TFBS) through genome. There're two options to get them:

  1. You can generate predictions using any motif scanning tool. E.g. you can use our tool SPRY-SARUS which is able to generate bed-file in necessary format. In this case, you can choose more or less strict thresholds for each prediction (i.e. more false positives vs more false negatives). Standard thresholds for HOCOMOCO motifs can be found at its downloads page (we, as HOCOMOCO authors, recommend thresholds corresponding to P-value of 0.0005).
  2. I had no experience with diffTF but it seems that authors prepared TFBS predictions and put them on their site. Please, take a look at this page of manual. If you don't need extra-flexibility in the generation of TFBS predictions, it can be the simplest way to proceed.

I guess, you're right that you need predictions of TFBS through genome. There're two options to get them:

  1. You can generate predictions using any motif scanning tool. E.g. you can use our tool SPRY-SARUS which is able to generate bed-file in necessary format. In this case you can choose more or less strict thresholds for each prediction (i.e. more false positives vs more false negatives). Standard thresholds for HOCOMOCO motifs can be found at its downloads page (we, as HOCOMOCO authors, recommend thresholds corresponding to P-value of 0.0005).
  2. I had no experience with diffTF but it seems that authors prepared TFBS predictions and put them on their site. Please, take a look at this page of manual. If you don't need extra-flexibility in generation of TFBS predictions, it can be the simplest way to proceed.

I guess you're right that you need predictions of transcription factor binding site (TFBS) through genome. There're two options to get them:

  1. You can generate predictions using any motif scanning tool. E.g. you can use our tool SPRY-SARUS which is able to generate bed-file in necessary format. In this case, you can choose more or less strict thresholds for each prediction (i.e. more false positives vs more false negatives). Standard thresholds for HOCOMOCO motifs can be found at its downloads page (we, as HOCOMOCO authors, recommend thresholds corresponding to P-value of 0.0005).
  2. I had no experience with diffTF but it seems that authors prepared TFBS predictions and put them on their site. Please, take a look at this page of manual. If you don't need extra-flexibility in the generation of TFBS predictions, it can be the simplest way to proceed.
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Ilya Vorontsov
Ilya Vorontsov
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I guess, you're right that you need predictions of TFBS through genome. There're two options to get them:

  1. You can generate predictions using any motif scanning tool. E.g. you can use our tool SPRY-SARUS which is able to generate bed-file in necessary format. In this case you can choose more or less strict thresholds for each prediction (i.e. more false positives vs more false negatives). Standard thresholds for HOCOMOCO motifs can be found at its downloads page (we, as HOCOMOCO authors, recommend thresholds corresponding to P-value of 0.0005).
  2. I had no experience with diffTF but it seems that authors prepared TFBS predictions and put them on their site. Please, take a look at this page of manual. If you don't need extra-flexibility in generation of TFBS predictions, it can be the simplest way to proceed.