DO NOT MERGE yet: Discuss fixes of #164 #168 #169

[ktrns]

Hi guys,

I have just talked to @JoseEspinosa, and we agreed that it would be best to create a pseudo-PR so we can next discuss our suggested changes after the summer break.

Mainly, we have fixed the following issues:

• Fixed issue Genome annotation (gene names) missing in IGV session file  #168 – The genome is again written out so that the IGV session file can be opened and used. This bug came with atacseq v2.0
• Fixed issue Peak calling parameters might not be ideal  #169 – Genome coverage tracks were generated & peaks were called based on fragments rather than reads, which is not correct for ATAC-seq analysis. This is fixed.
• Implemented issue Does nf-core/atacseq apply an offset to each ATAC-seq fragment? #164 (partly issue Adding the feature of shifting and splitting the reads #91) – A new parameter ‘--shift_reads’ adjusts the coordinates of the reads using deeptools/alignmentsieve. At the moment this only works for paired-end data and throws an error if applied to single-end data.

It would be fantastic if you could have a look at our changes. We are looking forward to discuss them with you.

Note to you and myself: I haven't adapted documentation yet.

Best wishes & thanks,
@ktrns and @andpet0101

[JoseEspinosa]

Adding the link to Harvard’s informatics help for future reference as suggested on this slack message.

[lpantano]

@ktrns , thanks for this! My group is interested to get this going, I will take things from this point, but If you are still working with this pipeline, I would love to catch up so we can coordinate efforts. let me know!