Is it possible to use fragment files as input? How to dictys for multiple samples?

[xgaoo]

Is it possible to use fragment files as input? How to use dictys for multiple samples?

[lingfeiwang]

Dictys uses wellington which does not accept fragment files. For multiple samples, see https://github.com/pinellolab/dictys/issues/31 and https://nbviewer.org/github/pinellolab/dictys/blob/a35fc8da150c8b175b0d5072e5f4bb7a827ab0e5/doc/tutorials/full-skin/notebooks/main2.ipynb?flush_cache=true#Optional:-Prepare-covariates. You no longer need to update Dictys because the changes are already incorporated in the master branch.

[nikostrasan]

Hello @xgaoo , We are very pleased to hear that you find our study insiprational. In addition to @lingfeiwang 's comment, unfortunately the strand information is required to run welligton footprinting, thus we recommend the use of iriginal bam files for dictys. As you mentioned, the data were acquired from another study, so the data should be deposited in GEO. It might be worth contacting GEO or the authors to obtain the original bam files. Best

[xgaoo]

Thank you for the explaination.

--------------原始邮件-------------- 发件人："nikos_trasan @.>; 发送时间：2023年9月28日(星期四) 凌晨1:16 收件人："pinellolab/dictys" @.>; 抄送："xgaoo @.>;"Mention @.>; 主题：Re: [pinellolab/dictys] Is it possible to use fragment files as input? How to dictys for multiple samples? (Issue #33)

Hello @xgaoo , We are very pleased that you find our study insiprational. In addition to @lingfeiwang 's comment, unfortunately the strand information is required to run welligton footprinting, thus we recommend the use of iriginal bam files for dictys. As you mentioned, the data were acquired from another study, so the data should be deposited in GEO. It might worth contacting GEO or the authors to obtain the original bam files. Best

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