Matthew Manion comments

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                                            Matthew Manion

Use tracks

> @mtxellrb A script for creating a track database from bigWig TF ChIP-seq data is now added :`create_cistarget_track_databases.py` > > https://github.com/aertslab/create_cisTarget_databases#create_cistarget_track_databasespy Hello @ghuls , I am running into an issue...

> @mtxellrb A script for creating a track database from bigWig TF ChIP-seq data is now added :`create_cistarget_track_databases.py`

> Your BED file is not in BED format: `chr start end name`: > > This will fix it: > > ``` > tail -n +2 fwf_gene_assignments.bed | awk -F...

> @mtxellrb A script for creating a track database from bigWig TF ChIP-seq data is now added :`create_cistarget_track_databases.py`

Okay so I was able to get the BED file into proper format, ![image](https://github.com/user-attachments/assets/73421d27-f738-446d-b514-2512c549132f) and ran create_cistarget_track_databases.py, ![image](https://github.com/user-attachments/assets/f1b4dadd-e02c-492d-895e-cff36528d7b4) but I am getting an issue with scoring the tracks for each...

> @mtxellrb A script for creating a track database from bigWig TF ChIP-seq data is now added :`create_cistarget_track_databases.py`

Thanks for your help,I dropped it to 4 columns and it seems to have ran and created the .feather rankings and scores.

> @mtxellrb A script for creating a track database from bigWig TF ChIP-seq data is now added :`create_cistarget_track_databases.py`

> Creating a track database also only would make some sense when you have several hundreds of tracks (even better thousands), instead of only 4. Can you clarify what you...

> @mtxellrb A script for creating a track database from bigWig TF ChIP-seq data is now added :`create_cistarget_track_databases.py`

@SeppeDeWinter Ideally, a database containing both motif and ChIP-seq scores. Thank you for the reply!

> @mtxellrb A script for creating a track database from bigWig TF ChIP-seq data is now added :`create_cistarget_track_databases.py`

@SeppeDeWinter Do you think it would be possible to use the outputs of a motif-discovery tool (we have successfully identified motifs in our ChIP-seq data using the MEME suite of...

> @mtxellrb A script for creating a track database from bigWig TF ChIP-seq data is now added :`create_cistarget_track_databases.py`

I will try that! We're using Nkx2.1 for our ChIP-seq

> @mtxellrb A script for creating a track database from bigWig TF ChIP-seq data is now added :`create_cistarget_track_databases.py`

We have seen some inconsistency between the Nkx2-1 motif between different databases, so one thing we' have done is to generate the motif from our own binding data in multiple...