SREQ-325 ready for submission

[AnnikaWeimer]

https://pulsar-encode.herokuapp.com/sequencing_requests/325/libraries_index

Hi Tao, those libraries can be submitted to the portal. Thanks!

[twang15]

Sub-tasks:

254

255

256

257

258

259

260

[twang15]

Hi Annika,

SREQ-325 are for snRNA experiments, which DCC requires strand specificity. Should we set them to forward or reverse for both reads or differently for each read?

Best, Tao

[AnnikaWeimer]

Yes, you can specify: forward

Thanks.

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Annika K. Weimer, PhD Project Lead ENCODE - Snyder lab

Stanford Medicine – Department of Genetics Center for Genomics and Personalized Medicine

@.**@.> +1 ‭(650) 724-4044

On Apr 29, 2021, at 10:15 PM, twang15 @.**@.>> wrote:

Hi Annika,

SREQ-325 are for snRNA experiments, which DCC requires strand specificity. Should we set them to forward or reverse for both reads or differently for each read?

Best, Tao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/StanfordBioinformatics/pulsar_lims/issues/251#issuecomment-829844026, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ASMM6ERVQ7P6FI4GDNOMTTTTLI4G7ANCNFSM43TLLSPQ.

[twang15]

For both reads?

[AnnikaWeimer]

It has 2 reads because it’s paired-end seq (which means the sequence is read from left to right and from right to left to get better coverage, but this is both on the same strand) but this is independent of the strand specificity. So yes, for both reads.

Thanks, Annika

---

Annika K. Weimer, PhD Project Lead ENCODE - Snyder lab

Stanford Medicine – Department of Genetics Center for Genomics and Personalized Medicine

@.**@.> +1 ‭(650) 724-4044

On May 3, 2021, at 10:16 AM, twang15 @.**@.>> wrote:

For both reads?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/StanfordBioinformatics/pulsar_lims/issues/251#issuecomment-831403879, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ASMM6ERTPSOAC7DGLJOTHV3TL3K5VANCNFSM43TLLSPQ.

[twang15]

It has 2 reads because it’s paired-end seq (which means the sequence is read from left to right and from right to left to get better coverage, but this is both on the same strand) but this is independent of the strand specificity. So yes, for both reads. Thanks, Annika …

Great, thanks for your confirmation.

[twang15]

Annika, for snRNA library,

the field "Strand Specific?" has to be set to true in the future. e.g., https://pulsar-encode.herokuapp.com/libraries/11477

[twang15]

Hi Annika,

SREQ-325 has been submitted successfully to the portal.

Best, Tao