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EMBL-Hentze-group / DEWSeq

R/Bioconductor package for e/iCLIP data analysis
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question about annotObj in DESeqDataSetFromSlidingWindows #6

Closed LoneKnightz closed 1 year ago

LoneKnightz commented 1 year ago

Hi,

I followed the tutorial from Htseq-clip and generated everything.

But the sliding windowed annotation file that Htseq-clip created is BED6 format.

It cannot be used for DESeqDataSetFromSlidingWindows as annotObj.

May I ask do you have any idea that can convert annotation from Htseq-clip to DESeqDataSetFromSlidingWindows recoginized annotObj ?

Distue commented 1 year ago

Hi,

Please use the htseq-clip mapToId function to convert the bed style annotation to a format which can be parsed by DEWSeq.

The flow diagram at https://htseq-clip.readthedocs.io/en/latest/ might help understanding the workflow.

The Bed6 format is primarily useful for visual inspection and counting, this additional step speeds up reading in large annotation files in R. We will make sure to add an error and explanation to DEWSeq. Thank you for bringing this up.

If you need anything else. Please feel free to contact us.

Best, Tom

LoneKnightz @.***> schrieb am Di., 29. Nov. 2022, 01:39:

Hi,

I followed the tutorial from Htseq-clip and generated everything.

But the sliding windowed annotation file that Htseq-clip created is BED6 format.

It cannot be used for DESeqDataSetFromSlidingWindows as annotObj.

May I ask do you have any idea that can convert annotation from Htseq-clip to DESeqDataSetFromSlidingWindows recoginized annotObj ?

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LoneKnightz commented 1 year ago

Thanks for reply. It really helped and my question got solved.

I followed the old flow diagram and I used wrong output file from Htseq-clip.