Using chrR ref genome with STAR #1
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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... |
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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...
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Give me a few days. I'll upload them, and then message you through GitHub. |
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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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Hi there, thank you so much for providing this resource. Have the .gtf files been uploaded? |
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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. |
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Was this GTF ever uploaded? I couldn't find it. |
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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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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<
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Was this GTF ever uploaded? I couldn't find it.
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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)
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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<
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Was this GTF ever uploaded? I couldn't find it.
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***@***.***
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<
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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<
>
#1 (comment)>,
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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<
> >
> #1 (comment)>,
>
> > or unsubscribe<
> >
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Try this link: https://upenn.box.com/s/sm2r2cnuryedorddcwfw60z8dftbe2xm |
|
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
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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
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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
> <
#1 (comment)>,
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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
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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
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