Amplicon prep fix

[charles-cowart]

Fixed undetected merge conflict in a sample output file. Added eight new blank columns and reordered them as requested by the wet-lab. Sample output file added to test_output for reference.

[charles-cowart]

test_output/amplicon/2021_08_17_THDMI-4-6_samplesheet.csv contains a merge conflict that was never resolved. This was probably overlooked because there aren't unittests associated with the iPython notebooks. Also, since there are a large number of changes, the diff wouldn’t appear in GitHub during a code review by default.

Resolved the merge conflict, preferring rows in [Data] with I7_Index_ID values like ‘515rcbc0’ over ‘EukBr_Hiseq_0017’. Observed that the indexes also changed for each sample. For example, ‘X00180471’ now has index ‘AGCCTTCGTCGC’ instead of ‘ACGAGACTGATT’. I believe this is normal behavior. Can @ahdilmore or @ElDeveloper please confirm? Thanks! Observed that values for I5_Index_ID, index2, and Well_description are also empty.

[charles-cowart]

Since Amplicon prep-files are currently generated by the Ipython notebook, I modified it to reorder the columns as mentioned in https://github.com/biocore/metagenomics_pooling_notebook/issues/54#issue-1069067398. As requested by the wet-lab, I've introduced the new columns with blank values that they will fill in as needed.

Ultimately this would be good to resolve as discussed in https://github.com/biocore/metagenomics_pooling_notebook/issues/40

[charles-cowart]

Adding @antgonza just to keep him in the loop. It doesn't warrant more than one person to review, IMHO.

[charles-cowart]

No unittests were added since we don't appear to be doing that for the notebooks. IMHO it would be good to be testing this functionality in the future.

[ahdilmore]

Resolved the merge conflict, preferring rows in [Data] with I7_Index_ID values like ‘515rcbc0’ over ‘EukBr_Hiseq_0017’. Observed that the indexes also changed for each sample. For example, ‘X00180471’ now has index ‘AGCCTTCGTCGC’ instead of ‘ACGAGACTGATT’. I believe this is normal behavior. Can @ahdilmore or @ElDeveloper please confirm? Thanks! Observed that values for I5_Index_ID, index2, and Well_description are also empty.

I think this is expected, but it might be best to confirm with the wet lab. Thank you for getting this done, Charlie!

[mmbryant23]

not sure if replying to this or directly works better (sorry) -

AGCCTTCGTCGC should be the correct barcode for X00180471 for 16s - we'll keep an eye on this when we test

On Mon, Dec 6, 2021 at 9:57 AM Hazel Dilmore @.***> wrote:

Resolved the merge conflict, preferring rows in [Data] with I7_Index_ID values like ‘515rcbc0’ over ‘EukBr_Hiseq_0017’. Observed that the indexes also changed for each sample. For example, ‘X00180471’ now has index ‘AGCCTTCGTCGC’ instead of ‘ACGAGACTGATT’. I believe this is normal behavior. Can @ahdilmore https://github.com/ahdilmore or @ElDeveloper https://github.com/ElDeveloper please confirm? Thanks! Observed that values for I5_Index_ID, index2, and Well_description are also empty.

I think this is expected, but it might be best to confirm with the wet lab. Thank you for getting this done, Charlie!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/biocore/metagenomics_pooling_notebook/pull/56#issuecomment-987016317, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVY3ITTHMOA3HDFXD4N75QLUPT2QZANCNFSM5JNKVLPA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[mmbryant23]

Thanks MacKenzie!

From: MacKenzie Bryant @.> Date: Monday, December 6, 2021 at 10:08 AM To: biocore/metagenomics_pooling_notebook @.>, Amanda H Dilmore @.>, Charles Cowart @.> Cc: biocore/metagenomics_pooling_notebook @.>, Subscribed @.> Subject: Re: [biocore/metagenomics_pooling_notebook] Amplicon prep fix (PR #56) not sure if replying to this or directly works better (sorry) -

AGCCTTCGTCGC should be the correct barcode for X00180471 for 16s - we'll keep an eye on this when we test

On Mon, Dec 6, 2021 at 9:57 AM Hazel Dilmore @.**@.>> wrote:

Resolved the merge conflict, preferring rows in [Data] with I7_Index_ID values like ‘515rcbc0’ over ‘EukBr_Hiseq_0017’. Observed that the indexes also changed for each sample. For example, ‘X00180471’ now has index ‘AGCCTTCGTCGC’ instead of ‘ACGAGACTGATT’. I believe this is normal behavior. Can @ahdilmorehttps://urldefense.com/v3/__https:/github.com/ahdilmore__;!!LLK065n_VXAQ!3rG-VeuL1UQmgyx3Ebo-mSSjfeVMHzlHBXwtklyWXw9v0DxAMh-U08nBnAZz4KkvOA$ or @ElDeveloperhttps://urldefense.com/v3/__https:/github.com/ElDeveloper__;!!LLK065n_VXAQ!3rG-VeuL1UQmgyx3Ebo-mSSjfeVMHzlHBXwtklyWXw9v0DxAMh-U08nBnAYUsMvdJA$ please confirm? Thanks! Observed that values for I5_Index_ID, index2, and Well_description are also empty.

I think this is expected, but it might be best to confirm with the wet lab. Thank you for getting this done, Charlie!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/biocore/metagenomics_pooling_notebook/pull/56*issuecomment-987016317__;Iw!!LLK065n_VXAQ!3rG-VeuL1UQmgyx3Ebo-mSSjfeVMHzlHBXwtklyWXw9v0DxAMh-U08nBnAbzQr1kuA$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AVY3ITTHMOA3HDFXD4N75QLUPT2QZANCNFSM5JNKVLPA__;!!LLK065n_VXAQ!3rG-VeuL1UQmgyx3Ebo-mSSjfeVMHzlHBXwtklyWXw9v0DxAMh-U08nBnAaKiGr8oA$. Triage notifications on the go with GitHub Mobile for iOShttps://urldefense.com/v3/__https:/apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675__;!!LLK065n_VXAQ!3rG-VeuL1UQmgyx3Ebo-mSSjfeVMHzlHBXwtklyWXw9v0DxAMh-U08nBnAYUAlgh8g$ or Androidhttps://urldefense.com/v3/__https:/play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign*3Dnotification-email*26utm_medium*3Demail*26utm_source*3Dgithub__;JSUlJSU!!LLK065n_VXAQ!3rG-VeuL1UQmgyx3Ebo-mSSjfeVMHzlHBXwtklyWXw9v0DxAMh-U08nBnAb8shKcKg$.

[charles-cowart]

Resolved the merge conflict, preferring rows in [Data] with I7_Index_ID values like ‘515rcbc0’ over ‘EukBr_Hiseq_0017’. Observed that the indexes also changed for each sample. For example, ‘X00180471’ now has index ‘AGCCTTCGTCGC’ instead of ‘ACGAGACTGATT’. I believe this is normal behavior. Can @ahdilmore or @ElDeveloper please confirm? Thanks! Observed that values for I5_Index_ID, index2, and Well_description are also empty.

I think this is expected, but it might be best to confirm with the wet lab. Thank you for getting this done, Charlie!

My pleasure! Thank you guys for confirming!

[charles-cowart]

@ElDeveloper Thanks for your patience! I've migrated the new code into metapool and updated the tests.

[ElDeveloper]

Thans @charles-cowart