Deduplication error

[yaaminiv]

Using the same code from Steven's lab notebook for deduplicate_bismark. Got the following error:

There is nothing in the help menu that says I need to specify a number for -p!

Did I misinterpret something?

[yaaminiv]

Used wrong command. Clearly not thinking this morning.

[sr320]

Yep

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On Tue, May 8, 2018 at 10:48 AM Yaamini Venkataraman < ***@***.***> wrote: Closed #252 <#252>. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#252 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEPHt3qV7rRh4niGCk3LJC5uctRMY0dgks5twdpHgaJpZM4T3EKR> .

[yaaminiv]

I have a REAL error this time

Jupyter notebook

The files from the bismark alignment step are apparently not compatible with correct methylation extraction, and I need to use unsorted files instead...Is the --barcode argument something that can remedy this, or do I need to redo the alignment?

[sr320]

Likely because when you ran alignment you did not indicate paired-end reads

[sr320]

Also you should get in habit of writing standard error out to file so notebook can be viewed more readily.

[yaaminiv]

I assume this means I need to re-run my alignment?

[sr320]

Yep

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On Tue, May 8, 2018 at 11:16 AM Yaamini Venkataraman < ***@***.***> wrote: I assume this means I need to re-run my alignment? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#252 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEPHtzcAwOtDXdIS0yvOPbTLIxiAQUSZks5tweCpgaJpZM4T3EKR> .

[yaaminiv]

Great. I will rerun the alignment on the full data.