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SchulzLab / EpigenomeAnalysisTutorial-2020

This website contains material for an epigenome analysis tutorial that covers ATAC-seq analysis and integration with TF motifs and gene expression
MIT License
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Index file needs an update? ./data/nf_core_atacseq/Cardiac.mRp.clN.sorted.bam.bai #5

Closed skarunan closed 4 years ago

skarunan commented 4 years ago

I get the warning message in steps 2.3, 2.4 and 4.1: The index file is older than the data file: ./data/nf_core_atacseq/Cardiac.mRp.clN.sorted.bam.bai

In 4.1 specially this warning is printed out 100s of time after the message generating signal for condition cardiac.

lzj1769 commented 4 years ago

this is a warning message about bam file index and can be ignored. I will add it to the docs.

lzj1769 commented 4 years ago

@skarunan

actually, we can try to generate new index files by:

samtools index ./EpigenomeAnalysisTutorial-2020/data/nf_core_atacseq/hESC.mRp.clN.sorted.bam
samtools index ./EpigenomeAnalysisTutorial-2020/data/nf_core_atacseq/Cardiac.mRp.clN.sorted.bam

can you do this? or I can do it and send the new index files to you.

skarunan commented 4 years ago

could you please send the new index files?

lzj1769 commented 4 years ago

you can download them from here: https://www.dropbox.com/sh/5aq3usob9pbo1rr/AADd3XNUbuCvyAZ01UIv3K5aa?dl=0

but looks like the new index files are exactly the same as the old ones, as they have the same hash code. anyway, if the warning message still exists, I will add some comments regarding this.

skarunan commented 4 years ago

Thanks, it's fixed now!