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vikramparalkar / rDNA-Mapping-Genomes

Human and mouse genome assemblies customized for rDNA mapping
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Using chrR ref genome with STAR #1

Open LucasMcNU opened 9 months ago

LucasMcNU commented 9 months ago

Hi, Thank you for putting these reference genomes together! They've been very helpful for my work.

I'd like to use hg38-rDNA_v1.0.fa to map an RNAseq dataset using STAR. How should the annotation file, hg38-rDNA_v1.0.bed, be adapted for compatibility with STAR's .gtf format?

Best

vikramparalkar commented 9 months ago

Hello, after the publication of this manuscript, we generated GTF files for RNA-seq mapping. Would you like us to share them with you?

We could actually just deposit them to this GitHub, so that they're available to all...

LucasMcNU commented 9 months ago

Yes please! I would love that.

On Thu, Feb 1, 2024 at 1:17 PM Vikram Paralkar Laboratory < @.***> wrote:

Hello, after the publication of this manuscript, we generated GTF files for RNA-seq mapping. Would you like us to share them with you?

We could actually just deposit them to this GitHub, so that they're available to all...

— Reply to this email directly, view it on GitHub https://github.com/vikramparalkar/rDNA-Mapping-Genomes/issues/1#issuecomment-1922051152, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVDTNYYK4ZYCFIVXHNVCDADYRPS3JAVCNFSM6AAAAABCTNSJCGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRSGA2TCMJVGI . You are receiving this because you authored the thread.Message ID: @.***>

vikramparalkar commented 9 months ago

Give me a few days. I'll upload them, and then message you through GitHub.

LucasMcNU commented 9 months ago

Great, thank you so much. We will of course cite you in our publication.

On Thu, Feb 1, 2024 at 1:18 PM Vikram Paralkar Laboratory < @.***> wrote:

Give me a few days. I'll upload them, and then message you through GitHub.

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multiomics23 commented 6 months ago

Hi there, thank you so much for providing this resource. Have the .gtf files been uploaded?

vikramparalkar commented 6 months ago

Our lab's computational biologist hasn't uploaded it yet, but we have it ready. What's your email address - I can share it with you that way.

LucasMcNU commented 2 months ago

Was this GTF ever uploaded? I couldn't find it.

vikramparalkar commented 2 months ago

Subin, could you refresh my memory on whether we ever updated the GTF to GitHub?

Lucas, could you just remind us whether you were looking for human or mouse? We could just directly share it with you for now (and we should also update on GitHub…).

Vikram

From: LucasMcNU @.> Reply-To: vikramparalkar/rDNA-Mapping-Genomes @.> Date: Wednesday, September 4, 2024 at 1:59 PM To: vikramparalkar/rDNA-Mapping-Genomes @.> Cc: "Paralkar, Vikram" @.>, Comment @.***> Subject: [External] Re: [vikramparalkar/rDNA-Mapping-Genomes] Using chrR ref genome with STAR (Issue #1)

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Was this GTF ever uploaded? I couldn't find it.

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LucasMcNU commented 2 months ago

Hi! human. We’re mapping some nascent rna seq and looking for unexpected rDNA reads. Best, Lucas

On Thu, Sep 5, 2024 at 9:22 AM Vikram Paralkar Laboratory < @.***> wrote:

Subin, could you refresh my memory on whether we ever updated the GTF to GitHub?

Lucas, could you just remind us whether you were looking for human or mouse? We could just directly share it with you for now (and we should also update on GitHub…).

Vikram

From: LucasMcNU @.> Reply-To: vikramparalkar/rDNA-Mapping-Genomes @.> Date: Wednesday, September 4, 2024 at 1:59 PM To: vikramparalkar/rDNA-Mapping-Genomes @.> Cc: "Paralkar, Vikram" @.>, Comment @.***> Subject: [External] Re: [vikramparalkar/rDNA-Mapping-Genomes] Using chrR ref genome with STAR (Issue #1)

You don't often get email from @.*** Learn why this is important< https://aka.ms/LearnAboutSenderIdentification>

Was this GTF ever uploaded? I couldn't find it.

— Reply to this email directly, view it on GitHub< https://github.com/vikramparalkar/rDNA-Mapping-Genomes/issues/1#issuecomment-2329669574>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/A2TPUHTI2N3OMEQAKB4EWRLZU5C7RAVCNFSM6AAAAABCTNSJCGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMRZGY3DSNJXGQ>.

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vikramparalkar commented 2 months ago

Lucas, can you share your direct email address? We’ll send you a Box link to download the GTF file. At some point, we will also upload it to GitHub.

Vikram

From: LucasMcNU @.> Reply-To: vikramparalkar/rDNA-Mapping-Genomes @.> Date: Thursday, September 5, 2024 at 12:27 PM To: vikramparalkar/rDNA-Mapping-Genomes @.> Cc: "Paralkar, Vikram" @.>, Comment @.***> Subject: [External] Re: [vikramparalkar/rDNA-Mapping-Genomes] Using chrR ref genome with STAR (Issue #1)

You don't often get email from @.*** Learn why this is importanthttps://aka.ms/LearnAboutSenderIdentification Hi! human. We’re mapping some nascent rna seq and looking for unexpected rDNA reads. Best, Lucas

On Thu, Sep 5, 2024 at 9:22 AM Vikram Paralkar Laboratory < @.***> wrote:

Subin, could you refresh my memory on whether we ever updated the GTF to GitHub?

Lucas, could you just remind us whether you were looking for human or mouse? We could just directly share it with you for now (and we should also update on GitHub…).

Vikram

From: LucasMcNU @.> Reply-To: vikramparalkar/rDNA-Mapping-Genomes @.> Date: Wednesday, September 4, 2024 at 1:59 PM To: vikramparalkar/rDNA-Mapping-Genomes @.> Cc: "Paralkar, Vikram" @.>, Comment @.***> Subject: [External] Re: [vikramparalkar/rDNA-Mapping-Genomes] Using chrR ref genome with STAR (Issue #1)

You don't often get email from @.*** Learn why this is important< https://aka.ms/LearnAboutSenderIdentification>

Was this GTF ever uploaded? I couldn't find it.

— Reply to this email directly, view it on GitHub< https://github.com/vikramparalkar/rDNA-Mapping-Genomes/issues/1#issuecomment-2329669574>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/A2TPUHTI2N3OMEQAKB4EWRLZU5C7RAVCNFSM6AAAAABCTNSJCGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMRZGY3DSNJXGQ>.

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LucasMcNU commented 2 months ago

@.***

Thank you!

On Thu, Sep 5, 2024 at 9:33 AM Vikram Paralkar Laboratory < @.***> wrote:

Lucas, can you share your direct email address? We’ll send you a Box link to download the GTF file. At some point, we will also upload it to GitHub.

Vikram

From: LucasMcNU @.> Reply-To: vikramparalkar/rDNA-Mapping-Genomes @.> Date: Thursday, September 5, 2024 at 12:27 PM To: vikramparalkar/rDNA-Mapping-Genomes @.> Cc: "Paralkar, Vikram" @.>, Comment @.***> Subject: [External] Re: [vikramparalkar/rDNA-Mapping-Genomes] Using chrR ref genome with STAR (Issue #1)

You don't often get email from @.*** Learn why this is important< https://aka.ms/LearnAboutSenderIdentification> Hi! human. We’re mapping some nascent rna seq and looking for unexpected rDNA reads. Best, Lucas

On Thu, Sep 5, 2024 at 9:22 AM Vikram Paralkar Laboratory < @.***> wrote:

Subin, could you refresh my memory on whether we ever updated the GTF to GitHub?

Lucas, could you just remind us whether you were looking for human or mouse? We could just directly share it with you for now (and we should also update on GitHub…).

Vikram

From: LucasMcNU @.> Reply-To: vikramparalkar/rDNA-Mapping-Genomes @.> Date: Wednesday, September 4, 2024 at 1:59 PM To: vikramparalkar/rDNA-Mapping-Genomes @.> Cc: "Paralkar, Vikram" @.>, Comment @.***> Subject: [External] Re: [vikramparalkar/rDNA-Mapping-Genomes] Using chrR ref genome with STAR (Issue #1)

You don't often get email from @.*** Learn why this is important< https://aka.ms/LearnAboutSenderIdentification>

Was this GTF ever uploaded? I couldn't find it.

— Reply to this email directly, view it on GitHub<

https://github.com/vikramparalkar/rDNA-Mapping-Genomes/issues/1#issuecomment-2329669574>,

or unsubscribe<

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LucasMcNU commented 2 months ago

Hi, Just following up on this - was it loaded to Github? I haven't recieved an email with the GTF. Thank you again! Lucas

On Thu, Sep 5, 2024 at 9:47 AM Lucas Carter < @.***> wrote:

@.***

Thank you!

On Thu, Sep 5, 2024 at 9:33 AM Vikram Paralkar Laboratory < @.***> wrote:

Lucas, can you share your direct email address? We’ll send you a Box link to download the GTF file. At some point, we will also upload it to GitHub.

Vikram

From: LucasMcNU @.> Reply-To: vikramparalkar/rDNA-Mapping-Genomes @.> Date: Thursday, September 5, 2024 at 12:27 PM To: vikramparalkar/rDNA-Mapping-Genomes @.> Cc: "Paralkar, Vikram" @.>, Comment @.***> Subject: [External] Re: [vikramparalkar/rDNA-Mapping-Genomes] Using chrR ref genome with STAR (Issue #1)

You don't often get email from @.*** Learn why this is important< https://aka.ms/LearnAboutSenderIdentification> Hi! human. We’re mapping some nascent rna seq and looking for unexpected rDNA reads. Best, Lucas

On Thu, Sep 5, 2024 at 9:22 AM Vikram Paralkar Laboratory < @.***> wrote:

Subin, could you refresh my memory on whether we ever updated the GTF to GitHub?

Lucas, could you just remind us whether you were looking for human or mouse? We could just directly share it with you for now (and we should also update on GitHub…).

Vikram

From: LucasMcNU @.> Reply-To: vikramparalkar/rDNA-Mapping-Genomes @.> Date: Wednesday, September 4, 2024 at 1:59 PM To: vikramparalkar/rDNA-Mapping-Genomes @.> Cc: "Paralkar, Vikram" @.>, Comment @.***> Subject: [External] Re: [vikramparalkar/rDNA-Mapping-Genomes] Using chrR ref genome with STAR (Issue #1)

You don't often get email from @.*** Learn why this is important< https://aka.ms/LearnAboutSenderIdentification>

Was this GTF ever uploaded? I couldn't find it.

— Reply to this email directly, view it on GitHub<

https://github.com/vikramparalkar/rDNA-Mapping-Genomes/issues/1#issuecomment-2329669574>,

or unsubscribe<

https://github.com/notifications/unsubscribe-auth/A2TPUHTI2N3OMEQAKB4EWRLZU5C7RAVCNFSM6AAAAABCTNSJCGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMRZGY3DSNJXGQ>.

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vikramparalkar commented 2 months ago

Try this link: https://upenn.box.com/s/sm2r2cnuryedorddcwfw60z8dftbe2xm

LucasMcNU commented 2 months ago

Seems that the file is unavailable there or inaccessible for me

[image: image.png]

On Thu, Sep 12, 2024 at 8:45 AM Vikram Paralkar Laboratory < @.***> wrote:

Try this link: https://upenn.box.com/s/sm2r2cnuryedorddcwfw60z8dftbe2xm

— Reply to this email directly, view it on GitHub https://github.com/vikramparalkar/rDNA-Mapping-Genomes/issues/1#issuecomment-2346649134, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVDTNY4JE3EPO2IT4OACWF3ZWGZKXAVCNFSM6AAAAABCTNSJCGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBWGY2DSMJTGQ . You are receiving this because you authored the thread.Message ID: @.***>

vikramparalkar commented 2 months ago

How about this link: https://www.dropbox.com/scl/fi/lme7nvue71l6dtf6msp5a/20220806_hg38_refseq_chrR_KY962518.1_35500cut_renamed.gtf.gz?rlkey=3mvm59o38h45qqwhp32zllet4&dl=0

Vikram

From: LucasMcNU @.> Reply-To: vikramparalkar/rDNA-Mapping-Genomes @.> Date: Thursday, September 12, 2024 at 12:33 PM To: vikramparalkar/rDNA-Mapping-Genomes @.> Cc: "Paralkar, Vikram" @.>, Comment @.***> Subject: [External] Re: [vikramparalkar/rDNA-Mapping-Genomes] Using chrR ref genome with STAR (Issue #1)

Seems that the file is unavailable there or inaccessible for me

[image: image.png]

On Thu, Sep 12, 2024 at 8:45 AM Vikram Paralkar Laboratory < @.***> wrote:

Try this link: https://upenn.box.com/s/sm2r2cnuryedorddcwfw60z8dftbe2xm

— Reply to this email directly, view it on GitHub https://github.com/vikramparalkar/rDNA-Mapping-Genomes/issues/1#issuecomment-2346649134, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVDTNY4JE3EPO2IT4OACWF3ZWGZKXAVCNFSM6AAAAABCTNSJCGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBWGY2DSMJTGQ . You are receiving this because you authored the thread.Message ID: @.***>

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LucasMcNU commented 2 months ago

success!

On Thu, Sep 12, 2024 at 11:36 AM Vikram Paralkar Laboratory < @.***> wrote:

How about this link: https://www.dropbox.com/scl/fi/lme7nvue71l6dtf6msp5a/20220806_hg38_refseq_chrR_KY962518.1_35500cut_renamed.gtf.gz?rlkey=3mvm59o38h45qqwhp32zllet4&dl=0

Vikram

From: LucasMcNU @.> Reply-To: vikramparalkar/rDNA-Mapping-Genomes @.> Date: Thursday, September 12, 2024 at 12:33 PM To: vikramparalkar/rDNA-Mapping-Genomes @.> Cc: "Paralkar, Vikram" @.>, Comment @.***> Subject: [External] Re: [vikramparalkar/rDNA-Mapping-Genomes] Using chrR ref genome with STAR (Issue #1)

Seems that the file is unavailable there or inaccessible for me

[image: image.png]

On Thu, Sep 12, 2024 at 8:45 AM Vikram Paralkar Laboratory < @.***> wrote:

Try this link: https://upenn.box.com/s/sm2r2cnuryedorddcwfw60z8dftbe2xm

— Reply to this email directly, view it on GitHub < https://github.com/vikramparalkar/rDNA-Mapping-Genomes/issues/1#issuecomment-2346649134>,

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vikramparalkar commented 2 months ago

Great! Let us know how it works.

Vikram

From: LucasMcNU @.> Reply-To: vikramparalkar/rDNA-Mapping-Genomes @.> Date: Thursday, September 12, 2024 at 2:48 PM To: vikramparalkar/rDNA-Mapping-Genomes @.> Cc: "Paralkar, Vikram" @.>, Comment @.***> Subject: [External] Re: [vikramparalkar/rDNA-Mapping-Genomes] Using chrR ref genome with STAR (Issue #1)

success!

On Thu, Sep 12, 2024 at 11:36 AM Vikram Paralkar Laboratory < @.***> wrote:

How about this link: https://www.dropbox.com/scl/fi/lme7nvue71l6dtf6msp5a/20220806_hg38_refseq_chrR_KY962518.1_35500cut_renamed.gtf.gz?rlkey=3mvm59o38h45qqwhp32zllet4&dl=0

Vikram

From: LucasMcNU @.> Reply-To: vikramparalkar/rDNA-Mapping-Genomes @.> Date: Thursday, September 12, 2024 at 12:33 PM To: vikramparalkar/rDNA-Mapping-Genomes @.> Cc: "Paralkar, Vikram" @.>, Comment @.***> Subject: [External] Re: [vikramparalkar/rDNA-Mapping-Genomes] Using chrR ref genome with STAR (Issue #1)

Seems that the file is unavailable there or inaccessible for me

[image: image.png]

On Thu, Sep 12, 2024 at 8:45 AM Vikram Paralkar Laboratory < @.***> wrote:

Try this link: https://upenn.box.com/s/sm2r2cnuryedorddcwfw60z8dftbe2xm

— Reply to this email directly, view it on GitHub < https://github.com/vikramparalkar/rDNA-Mapping-Genomes/issues/1#issuecomment-2346649134>,

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bug1303 commented 4 days ago

Any chance that you will actually deposit the gtf files here? I think it would be helpful for many! I'd be interested on using STAR on the modified genome for mm10.