Interested in using transMap V5 for our Great Ape Study (panTro6, gorGor5, hg38)

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Castro-Pacheco, Nathan

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Apr 26, 2021, 12:53:30 PM4/26/21

to gen...@soe.ucsc.edu

Hi there UCSC Genome Institute Representative,

I'm a researcher at Cold Spring Harbor Laboratory in Long Island NY interested in deriving a common set of transcripts (with Ensembl IDs) between panTro6, gorGor5, and hg38 to aid in a Great Ape study we are working on.

Initially, we converted panTro6.ensembl.transMapV5.bigPsl & gorGor5.ensembl.transMapV5.bigPsl to psl format using bigPslToPsl and only kept alignments in each where qName (column 10) began with hg38 meaning the alignment was to a human transcript.

After extracting aligned human transcripts for both panTro6 and gorGor5 we found the intersection of these Transcript IDs thereby giving us a common set between all three species.

We wanted to use the same approach for panTro6 and gorGor5 of extracting transcripts from alignments to a target species but this would require that:

- For panTro6 derivation: Both gorGor5.ensembl.transMapV5.bigPsl & hg38.ensembl.transMapV5.bigPsl contain alignments to panTro6

- For gorGor5 based derivation: Both panTro6.ensembl.transMapV5.bigPsl & hg38.ensembl.transMapV5.bigPsl contain alignments to gorGor5

However, neither of these cases are met as both panTro6 and gorGor5 only contain alignments to mm10 and hg38 and hg38 does not contain alignments to either panTro6 or gorGor5.

With that said, we were wondering if your team at UCSC would be interested in deriving these alignments between transcripts of the three species of interest or sharing the pipeline used to derived TransMap files in order to allow us to do this ourselves. Either way, we'd be happy to include UCSC Genome Institute in our acknowledgments of any publications we produce using TransMap V5 data.

Hopefully, we'll be able to derive these alignments in some way or another

Thanks,

Nathan Castro Pacheco<https://www.linkedin.com/in/nathan-castro-pacheco/>

Dobin Lab <https://www.cshl.edu/research/faculty-staff/alexander-dobin/> @ CSHL<https://www.cshl.edu/>

Daniel Schmelter

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May 7, 2021, 8:15:14 PM5/7/21

to Castro-Pacheco, Nathan, gen...@soe.ucsc.edu

Hello Nathan,

Thanks for emailing the Genome Browser team and for your patience with this response.

We are working on updating TransMap tracks still, and we have some pre-release data that may suit your purposes. These tracks are on TransMap v6 and they have additional information that could include your species. Since this is pre-release data, it has not been quality-verified and may have an incomplete or not-updated track description page. The process to create the data should generally be valid.

https://genome-preview.ucsc.edu/cgi-bin/hgTrackUi?db=gorGor5&g=transMapV6
https://genome-preview.ucsc.edu/cgi-bin/hgTrackUi?db=panTro6&g=transMapV6

You are probably already aware of our offerings on hg38. There is no pre-release TransMap data for this assembly, only the V5.

https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=transMapV5

As for when this, or similar data will be released, we cannot give a timeline. It is a priority to get to this at some point. I hope this was helpful.

For further communication, please reply-all to gen...@soe.ucsc.edu. Those emails are archived in a public help forum. For private questions, you may send emails instead to genom...@soe.ucsc.edu.

All the best,

Daniel Schmelter
UCSC Genome Browser

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Castro-Pacheco, Nathan

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May 11, 2021, 2:23:33 AM5/11/21

to Daniel Schmelter, gen...@soe.ucsc.edu

Hi Daniel,

Thanks for the information. It's great to see the Genome Browser team is working on the next version of TransMap. Given that the data is pre-release would there be any way for our team to gain access to the non-quality verified version of these tracks in the form of a bigPsl? Since we need these tracks primarily to determine if our current method for deriving an equivalent set of isoforms between species is introducing any biases, non quality-verified data should serve our purposes!

If this is not possible I completely understand and appreciate your response regardless!

Thanks,

Nathan Castro Pacheco<https://www.linkedin.com/in/nathan-castro-pacheco/>
Dobin Lab <https://www.cshl.edu/research/faculty-staff/alexander-dobin/> @ CSHL<https://www.cshl.edu/>

________________________________
From: Daniel Schmelter <dsch...@ucsc.edu>
Sent: Friday, May 7, 2021 8:15:00 PM
To: Castro-Pacheco, Nathan
Cc: gen...@soe.ucsc.edu
Subject: Re: [genome] Interested in using transMap V5 for our Great Ape Study (panTro6, gorGor5, hg38)

Hello Nathan,

Thanks for emailing the Genome Browser team and for your patience with this response.

We are working on updating TransMap tracks still, and we have some pre-release data that may suit your purposes. These tracks are on TransMap v6 and they have additional information that could include your species. Since this is pre-release data, it has not been quality-verified and may have an incomplete or not-updated track description page. The process to create the data should generally be valid.

You are probably already aware of our offerings on hg38. There is no pre-release TransMap data for this assembly, only the V5.

As for when this, or similar data will be released, we cannot give a timeline. It is a priority to get to this at some point. I hope this was helpful.

For further communication, please reply-all to gen...@soe.ucsc.edu<mailto:gen...@soe.ucsc.edu>. Those emails are archived in a public help forum. For private questions, you may send emails instead to genom...@soe.ucsc.edu<mailto:genom...@soe.ucsc.edu>.

All the best,

Daniel Schmelter
UCSC Genome Browser

On Mon, Apr 26, 2021 at 9:53 AM Castro-Pacheco, Nathan <cas...@cshl.edu<mailto:cas...@cshl.edu>> wrote:
Hi there UCSC Genome Institute Representative,

I'm a researcher at Cold Spring Harbor Laboratory in Long Island NY interested in deriving a common set of transcripts (with Ensembl IDs) between panTro6, gorGor5, and hg38 to aid in a Great Ape study we are working on.

Initially, we converted panTro6.ensembl.transMapV5.bigPsl & gorGor5.ensembl.transMapV5.bigPsl to psl format using bigPslToPsl and only kept alignments in each where qName (column 10) began with hg38 meaning the alignment was to a human transcript.

After extracting aligned human transcripts for both panTro6 and gorGor5 we found the intersection of these Transcript IDs thereby giving us a common set between all three species.

We wanted to use the same approach for panTro6 and gorGor5 of extracting transcripts from alignments to a target species but this would require that:

- For panTro6 derivation: Both gorGor5.ensembl.transMapV5.bigPsl & hg38.ensembl.transMapV5.bigPsl contain alignments to panTro6

- For gorGor5 based derivation: Both panTro6.ensembl.transMapV5.bigPsl & hg38.ensembl.transMapV5.bigPsl contain alignments to gorGor5

However, neither of these cases are met as both panTro6 and gorGor5 only contain alignments to mm10 and hg38 and hg38 does not contain alignments to either panTro6 or gorGor5.

With that said, we were wondering if your team at UCSC would be interested in deriving these alignments between transcripts of the three species of interest or sharing the pipeline used to derived TransMap files in order to allow us to do this ourselves. Either way, we'd be happy to include UCSC Genome Institute in our acknowledgments of any publications we produce using TransMap V5 data.

Hopefully, we'll be able to derive these alignments in some way or another

Thanks,

Dobin Lab <https://www.cshl.edu/research/faculty-staff/alexander-dobin/> @ CSHL<https://www.cshl.edu/>

--

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You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.

To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu<mailto:genome%2Bunsu...@soe.ucsc.edu>.
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Daniel Schmelter

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May 12, 2021, 6:26:56 PM5/12/21

to Castro-Pacheco, Nathan, gen...@soe.ucsc.edu

Hello Nathan,

You can find the download files requested at the following link:

https://hgdownload-test.gi.ucsc.edu/gbdb/

Since they are pre-release, we will remove them from that location after 1 week. Be sure to save them locally before that. We hope to get them out officially before long.

All the best,

Daniel Schmelter

UCSC Genome Browser

Castro-Pacheco, Nathan

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May 13, 2021, 3:25:53 PM5/13/21

to Daniel Schmelter, gen...@soe.ucsc.edu

Hi Daniel,

Great thanks! I've downloaded them and was wondering if you happen to know what version of hg38 the human files are for as I'm looking for the GTF associated with that assembly.

Thanks,

Nathan Castro-Pacheco

Dobin Lab @ CSHL

________________________________
From: Daniel Schmelter <dsch...@ucsc.edu>

Sent: Wednesday, May 12, 2021 6:26:37 PM

To: Castro-Pacheco, Nathan
Cc: gen...@soe.ucsc.edu
Subject: Re: [genome] Interested in using transMap V5 for our Great Ape Study (panTro6, gorGor5, hg38)

Hello Nathan,

You can find the download files requested at the following link:

https://hgdownload-test.gi.ucsc.edu/gbdb/<https://urldefense.proofpoint.com/v2/url?u=https-3A__hgdownload-2Dtest.gi.ucsc.edu_gbdb_&d=DwMFaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=WN1C9rezXLyD-Cev1xw3-A&m=7G8fLtcEDjzkabTtnl4eQzw_hL3jLAIji4tzteN-_Xo&s=WV9RiwxTsHIJVIfnn90XdNBqJdozwmps0ezTTYJkHfc&e=>

Since they are pre-release, we will remove them from that location after 1 week. Be sure to save them locally before that. We hope to get them out officially before long.

All the best,
Daniel Schmelter
UCSC Genome Browser

On Mon, May 10, 2021 at 8:30 AM Castro-Pacheco, Nathan <cas...@cshl.edu<mailto:cas...@cshl.edu>> wrote:
Hi Daniel,

Thanks for the information. It's great to see the Genome Browser team is working on the next version of TransMap. Given that the data is pre-release would there be any way for our team to gain access to the non-quality verified version of these tracks in the form of a bigPsl? Since we need these tracks primarily to determine if our current method for deriving an equivalent set of isoforms between species is introducing any biases, non quality-verified data should serve our purposes!

If this is not possible I completely understand and appreciate your response regardless!

Thanks,

Dobin Lab <https://www.cshl.edu/research/faculty-staff/alexander-dobin/> @ CSHL<https://www.cshl.edu/>

________________________________

From: Daniel Schmelter <dsch...@ucsc.edu<mailto:dsch...@ucsc.edu>>

Sent: Friday, May 7, 2021 8:15:00 PM
To: Castro-Pacheco, Nathan

Cc: gen...@soe.ucsc.edu<mailto:gen...@soe.ucsc.edu>

Subject: Re: [genome] Interested in using transMap V5 for our Great Ape Study (panTro6, gorGor5, hg38)

Hello Nathan,

Thanks for emailing the Genome Browser team and for your patience with this response.

We are working on updating TransMap tracks still, and we have some pre-release data that may suit your purposes. These tracks are on TransMap v6 and they have additional information that could include your species. Since this is pre-release data, it has not been quality-verified and may have an incomplete or not-updated track description page. The process to create the data should generally be valid.

https://genome-preview.ucsc.edu/cgi-bin/hgTrackUi?db=gorGor5&g=transMapV6<https://urldefense.proofpoint.com/v2/url?u=https-3A__genome-2Dpreview.ucsc.edu_cgi-2Dbin_hgTrackUi-3Fdb-3DgorGor5-26g-3DtransMapV6&d=DwMFaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=WN1C9rezXLyD-Cev1xw3-A&m=7G8fLtcEDjzkabTtnl4eQzw_hL3jLAIji4tzteN-_Xo&s=7FTA48-QZiGCQ2L4TzevUrRG3UkGiVNNIb7-EdRsG_A&e=><https://urldefense.proofpoint.com/v2/url?u=https-3A__genome-2Dpreview.ucsc.edu_cgi-2Dbin_hgTrackUi-3Fdb-3DgorGor5-26g-3DtransMapV6&d=DwMFaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=WN1C9rezXLyD-Cev1xw3-A&m=pN6qEXsitc2PdIRFBUI1V7w3z4fFlXtX2oZzHGRAdx8&s=5rcgNMBdtqlp3zyNI1Y1Lrnuc0zLTaWOC2O8tWIT0JM&e=>
https://genome-preview.ucsc.edu/cgi-bin/hgTrackUi?db=panTro6&g=transMapV6<https://urldefense.proofpoint.com/v2/url?u=https-3A__genome-2Dpreview.ucsc.edu_cgi-2Dbin_hgTrackUi-3Fdb-3DpanTro6-26g-3DtransMapV6&d=DwMFaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=WN1C9rezXLyD-Cev1xw3-A&m=7G8fLtcEDjzkabTtnl4eQzw_hL3jLAIji4tzteN-_Xo&s=ryW5wTO6w5GC6Rh1LhmGOM6fE4zsOrY_is3wHPdoe-E&e=><https://urldefense.proofpoint.com/v2/url?u=https-3A__genome-2Dpreview.ucsc.edu_cgi-2Dbin_hgTrackUi-3Fdb-3DpanTro6-26g-3DtransMapV6&d=DwMFaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=WN1C9rezXLyD-Cev1xw3-A&m=pN6qEXsitc2PdIRFBUI1V7w3z4fFlXtX2oZzHGRAdx8&s=-MLHiXjHYxrEs1daS8mE0gZ3XV3i8GGhNwMVAT5P6dw&e=>

You are probably already aware of our offerings on hg38. There is no pre-release TransMap data for this assembly, only the V5.

https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=transMapV5<https://urldefense.proofpoint.com/v2/url?u=https-3A__genome.ucsc.edu_cgi-2Dbin_hgTrackUi-3Fdb-3Dhg38-26g-3DtransMapV5&d=DwMFaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=WN1C9rezXLyD-Cev1xw3-A&m=7G8fLtcEDjzkabTtnl4eQzw_hL3jLAIji4tzteN-_Xo&s=QXcwaEvSsEA6mjFHgp1Jm7Ehy6WEulYHQlM_s6lPCKg&e=><https://urldefense.proofpoint.com/v2/url?u=https-3A__genome.ucsc.edu_cgi-2Dbin_hgTrackUi-3Fdb-3Dhg38-26g-3DtransMapV5&d=DwMFaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=WN1C9rezXLyD-Cev1xw3-A&m=pN6qEXsitc2PdIRFBUI1V7w3z4fFlXtX2oZzHGRAdx8&s=Y9VGIXENgUz2hxkDtykabea6ybIlZ81GqzfWw60y9fk&e=>

As for when this, or similar data will be released, we cannot give a timeline. It is a priority to get to this at some point. I hope this was helpful.

For further communication, please reply-all to gen...@soe.ucsc.edu<mailto:gen...@soe.ucsc.edu><mailto:gen...@soe.ucsc.edu<mailto:gen...@soe.ucsc.edu>>. Those emails are archived in a public help forum. For private questions, you may send emails instead to genom...@soe.ucsc.edu<mailto:genom...@soe.ucsc.edu><mailto:genom...@soe.ucsc.edu<mailto:genom...@soe.ucsc.edu>>.

All the best,

Daniel Schmelter
UCSC Genome Browser

On Mon, Apr 26, 2021 at 9:53 AM Castro-Pacheco, Nathan <cas...@cshl.edu<mailto:cas...@cshl.edu><mailto:cas...@cshl.edu<mailto:cas...@cshl.edu>>> wrote:
Hi there UCSC Genome Institute Representative,

I'm a researcher at Cold Spring Harbor Laboratory in Long Island NY interested in deriving a common set of transcripts (with Ensembl IDs) between panTro6, gorGor5, and hg38 to aid in a Great Ape study we are working on.

Initially, we converted panTro6.ensembl.transMapV5.bigPsl & gorGor5.ensembl.transMapV5.bigPsl to psl format using bigPslToPsl and only kept alignments in each where qName (column 10) began with hg38 meaning the alignment was to a human transcript.

After extracting aligned human transcripts for both panTro6 and gorGor5 we found the intersection of these Transcript IDs thereby giving us a common set between all three species.

We wanted to use the same approach for panTro6 and gorGor5 of extracting transcripts from alignments to a target species but this would require that:

- For panTro6 derivation: Both gorGor5.ensembl.transMapV5.bigPsl & hg38.ensembl.transMapV5.bigPsl contain alignments to panTro6

- For gorGor5 based derivation: Both panTro6.ensembl.transMapV5.bigPsl & hg38.ensembl.transMapV5.bigPsl contain alignments to gorGor5

However, neither of these cases are met as both panTro6 and gorGor5 only contain alignments to mm10 and hg38 and hg38 does not contain alignments to either panTro6 or gorGor5.

With that said, we were wondering if your team at UCSC would be interested in deriving these alignments between transcripts of the three species of interest or sharing the pipeline used to derived TransMap files in order to allow us to do this ourselves. Either way, we'd be happy to include UCSC Genome Institute in our acknowledgments of any publications we produce using TransMap V5 data.

Hopefully, we'll be able to derive these alignments in some way or another

Thanks,

Nathan Castro Pacheco<https://www.linkedin.com/in/nathan-castro-pacheco/<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.linkedin.com_in_nathan-2Dcastro-2Dpacheco_&d=DwMFaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=WN1C9rezXLyD-Cev1xw3-A&m=7G8fLtcEDjzkabTtnl4eQzw_hL3jLAIji4tzteN-_Xo&s=gxO64Yzh2M5XHUtMikdePfflcVAiOOadtZo5zsJvNno&e=><https://urldefense.proofpoint.com/v2/url?u=https-3A__www.linkedin.com_in_nathan-2Dcastro-2Dpacheco_&d=DwMFaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=WN1C9rezXLyD-Cev1xw3-A&m=pN6qEXsitc2PdIRFBUI1V7w3z4fFlXtX2oZzHGRAdx8&s=Nqs4BC9zCj0mPxWzBXOE7-BUiZAgex-KT36TU0dUdlM&e=>>

To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu<mailto:genome%2Bunsu...@soe.ucsc.edu><mailto:genome%2Bunsu...@soe.ucsc.edu<mailto:genome%252Buns...@soe.ucsc.edu>>.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/968bee162e3f4e398189f70552ec6b97%40cshl.edu<https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_a_soe.ucsc.edu_d_msgid_genome_968bee162e3f4e398189f70552ec6b97-2540cshl.edu&d=DwMFaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=WN1C9rezXLyD-Cev1xw3-A&m=7G8fLtcEDjzkabTtnl4eQzw_hL3jLAIji4tzteN-_Xo&s=NlvY-CwfVW3jmKl6WjFbMkL7Wq3LWYqeHpcMCMzHUVw&e=><https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_a_soe.ucsc.edu_d_msgid_genome_968bee162e3f4e398189f70552ec6b97-2540cshl.edu&d=DwMFaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=WN1C9rezXLyD-Cev1xw3-A&m=pN6qEXsitc2PdIRFBUI1V7w3z4fFlXtX2oZzHGRAdx8&s=VsFzJPzLH9ysNQvsmgWqTvTR2fmtxS0bh2VdqsbjoXU&e=>.

Gerardo Perez

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May 14, 2021, 3:13:49 PM5/14/21

to Castro-Pacheco, Nathan, gen...@soe.ucsc.edu

Hello Nathan,

Thank you for your interest in the UCSC Genome Browser and your follow-up question about the hg38 version.

The human files correspond to the patch level p13 for hg38 (GRCh38.p13). The following blog post covers details on this patch release:
https://genomeref.blogspot.com/2019/03/grch38p13-has-been-released.html

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
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