Adding chain files for new assemblies

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Demayo, James

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Sep 5, 2023, 12:32:55 PM9/5/23
to gen...@soe.ucsc.edu
Dear UCSC Genome list,

I am interested in comparing orthologous genes for various species of Drosophila. Could the Genome staff help in producing chain and 2bit files for genome assemblies of Drosophila persimilis to Drosophila bipectinata?

Thank you very much for your help.

Sincerely,

Jimmy deMayo, PhD (he/him)

Postdoctoral Researcher
Ragland lab
University of Colorado Denver

Matthew Speir

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Sep 6, 2023, 4:15:00 PM9/6/23
to Demayo, James, gen...@soe.ucsc.edu
Hello, Jimmy.

Thank you for your request for LiftOver files.

We have now made these files for D. persimilis (GCF_003286085.1 - DperRS2 Oct. 2018)
Finally, you can view these genomes in the UCSC Genome Browser by clicking the link in the first column for these two species on this page: https://hgdownload.soe.ucsc.edu/hubs/invertebrate/index.html. (It's quite a long list, so I recommend searching for the GCF IDs directly.)

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.
---

Matthew Speir

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

Revealing life’s code.



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Demayo, James

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Sep 6, 2023, 6:36:05 PM9/6/23
to Matthew Speir, gen...@soe.ucsc.edu
Hi Matthew,

Thank you so much for your help. Would you mind sharing the command line script you used to generate the chain files? If not, can you share what parameters you set for creating them? 

Sincerely,

Jimmy deMayo, PhD (he/him)

Postdoctoral Researcher
Ragland lab
University of Colorado Denver
From: Matthew Speir <msp...@ucsc.edu>
Sent: Wednesday, September 6, 2023 2:14 PM
To: Demayo, James <JAMES....@UCDENVER.EDU>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] Adding chain files for new assemblies
 
[External Email - Use Caution]

Hiram Clawson

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Sep 6, 2023, 7:15:34 PM9/6/23
to Demayo, James, Matthew Speir, gen...@soe.ucsc.edu
Good Afternoon Dr. deMayo:

It is much more than a command to create the chain files, it is a process
of several steps, including a cluster operation for the pair-wise alignment.

First is a pair-wise alignment with lastz and parameters:

# lastz.v1.04.03 H=2000 --format=axt+
#
# hsp_threshold = 3000
# gapped_threshold = 3000
# x_drop = 910
# y_drop = 9400
# gap_open_penalty = 400
# gap_extend_penalty = 30
# A C G T
# A 91 -114 -31 -123
# C -114 100 -125 -31
# G -31 -125 100 -114
# T -123 -31 -114 91
# seed=1110100110010101111 w/transition
# step=1

Then, chaining with arguments:

axtChain -psl -minScore=5000 -linearGap=loose

passing the output of that through chainAntiRepeat.

Then chainPreNet through chainNet to netSyntenic and finally
netChainSubset to get the liftOver chain file:

chainPreNet GCF_018153845.1.GCF_003286085.1.all.chain.gz \
GCF_018153845.1.chrom.sizes.txt GCF_003286085.1.chrom.sizes.txt stdout \
| chainNet stdin -minSpace=1 GCF_018153845.1.chrom.sizes.txt \
GCF_003286085.1.chrom.sizes.txt stdout /dev/null \
| netSyntenic stdin noClass.net

netChainSubset noClass.net GCF_018153845.1.GCF_003286085.1.all.chain.gz stdout \
| chainStitchId stdin stdout | gzip -c > GCF_018153845.1.GCF_003286085.1.over.chain.gz

--Hiram

On 9/6/23 3:34 PM, Demayo, James wrote:
> Hi Matthew,
>
> Thank you so much for your help. Would you mind sharing the command line script you used to generate the chain files? If not, can you share what parameters you set for creating them?
>
> Sincerely,
>
> Jimmy deMayo, PhD (he/him)
>
> Postdoctoral Researcher
> Ragland lab
> University of Colorado Denver
> ________________________________
> From: Matthew Speir <msp...@ucsc.edu>
> Sent: Wednesday, September 6, 2023 2:14 PM
> To: Demayo, James <JAMES....@UCDENVER.EDU>
> Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
> Subject: Re: [genome] Adding chain files for new assemblies
>
> [External Email - Use Caution]
> Hello, Jimmy.
>
> Thank you for your request for LiftOver files.
>
> We have now made these files for D. persimilis (GCF_003286085.1<https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_003286085.1/> - DperRS2 Oct. 2018)
> and D. bipectinata (GCF_018153845.1<https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_018153845.1/> - ASM1815384v1 Apr. 2021) available our downloads server:
>
> Chain files:
> https://hgdownload.soe.ucsc.edu/hubs/GCF/018/153/845/GCF_018153845.1/liftOver/GCF_018153845.1ToGCF_003286085.1.over.chain.gz
> https://hgdownload.soe.ucsc.edu/hubs/GCF/003/286/085/GCF_003286085.1/liftOver/GCF_003286085.1ToGCF_018153845.1.over.chain.gz
>
> 2bit files:
> https://hgdownload.soe.ucsc.edu/hubs/GCF/018/153/845/GCF_018153845.1/GCF_018153845.1.2bit
> https://hgdownload.soe.ucsc.edu/hubs/GCF/003/286/085/GCF_003286085.1/GCF_003286085.1.2bit
>
> Finally, you can view these genomes in the UCSC Genome Browser by clicking the link in the first column for these two species on this page: https://hgdownload.soe.ucsc.edu/hubs/invertebrate/index.html. (It's quite a long list, so I recommend searching for the GCF IDs directly.)
>
> I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu<mailto: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<mailto:genom...@soe.ucsc.edu>.
> ---
>
> Matthew Speir
>
> UCSC Genome Browser, User Support
>
> UC Santa Cruz Genomics Institute<http://genomics.ucsc.edu/>

Demayo, James

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Sep 6, 2023, 7:31:11 PM9/6/23
to Hiram Clawson, Matthew Speir, gen...@soe.ucsc.edu
Hi Hiram,

Thank you for the pipeline. This is very helpful. Can you explain the rationale used for the parameters used during the alignment step?

Sincerely,

Jimmy deMayo, PhD (he/him)

Postdoctoral Researcher
Ragland lab
University of Colorado Denver
From: Hiram Clawson <hi...@soe.ucsc.edu>
Sent: Wednesday, September 6, 2023 5:15 PM
To: Demayo, James <JAMES....@UCDENVER.EDU>; Matthew Speir <msp...@ucsc.edu>
> We have now made these files for D. persimilis (GCF_003286085.1<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fdatasets%2Fgenome%2FGCF_003286085.1%2F&data=05%7C01%7CJAMES.DEMAYO%40ucdenver.edu%7C4e4c8f03c9024a45e5e508dbaf2f2b30%7C563337caa517421aaae01aa5b414fd7f%7C0%7C0%7C638296389635860385%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=jQeEmM5KFbUQ7g%2FW%2FFXMqwpsoF3U%2BFsoeE7S%2FIKItUw%3D&reserved=0> - DperRS2 Oct. 2018)
> and D. bipectinata (GCF_018153845.1<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fdatasets%2Fgenome%2FGCF_018153845.1%2F&data=05%7C01%7CJAMES.DEMAYO%40ucdenver.edu%7C4e4c8f03c9024a45e5e508dbaf2f2b30%7C563337caa517421aaae01aa5b414fd7f%7C0%7C0%7C638296389635860385%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=x5C9fF%2BGxnbfbY9NnJExh2BEs%2BLXcrl0VGH67sZccEQ%3D&reserved=0> - ASM1815384v1 Apr. 2021) available our downloads server:
>
> Chain files:
> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhgdownload.soe.ucsc.edu%2Fhubs%2FGCF%2F018%2F153%2F845%2FGCF_018153845.1%2FliftOver%2FGCF_018153845.1ToGCF_003286085.1.over.chain.gz&data=05%7C01%7CJAMES.DEMAYO%40ucdenver.edu%7C4e4c8f03c9024a45e5e508dbaf2f2b30%7C563337caa517421aaae01aa5b414fd7f%7C0%7C0%7C638296389635860385%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=81vZM6iDpoD%2BiCE1gxr3uXHNf4Or6FuORT1Pu%2F5i6Vo%3D&reserved=0
> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhgdownload.soe.ucsc.edu%2Fhubs%2FGCF%2F003%2F286%2F085%2FGCF_003286085.1%2FliftOver%2FGCF_003286085.1ToGCF_018153845.1.over.chain.gz&data=05%7C01%7CJAMES.DEMAYO%40ucdenver.edu%7C4e4c8f03c9024a45e5e508dbaf2f2b30%7C563337caa517421aaae01aa5b414fd7f%7C0%7C0%7C638296389635860385%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=xvbf85zozNAYhF5tdTBny0EE4GuVHs%2BYXmkzd9sUS7k%3D&reserved=0
>
> 2bit files:
> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhgdownload.soe.ucsc.edu%2Fhubs%2FGCF%2F018%2F153%2F845%2FGCF_018153845.1%2FGCF_018153845.1.2bit&data=05%7C01%7CJAMES.DEMAYO%40ucdenver.edu%7C4e4c8f03c9024a45e5e508dbaf2f2b30%7C563337caa517421aaae01aa5b414fd7f%7C0%7C0%7C638296389635860385%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=1ffHYUS6VGxBc%2B2ESYX89LdROS%2BcLGpAOZtrEMyBIhg%3D&reserved=0
> https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhgdownload.soe.ucsc.edu%2Fhubs%2FGCF%2F003%2F286%2F085%2FGCF_003286085.1%2FGCF_003286085.1.2bit&data=05%7C01%7CJAMES.DEMAYO%40ucdenver.edu%7C4e4c8f03c9024a45e5e508dbaf2f2b30%7C563337caa517421aaae01aa5b414fd7f%7C0%7C0%7C638296389635860385%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=9Zc2pvaDuKojWG2kKBXaDyBJQnPyw8SH90MDLvT1wvk%3D&reserved=0
>
> Finally, you can view these genomes in the UCSC Genome Browser by clicking the link in the first column for these two species on this page: https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhgdownload.soe.ucsc.edu%2Fhubs%2Finvertebrate%2Findex.html&data=05%7C01%7CJAMES.DEMAYO%40ucdenver.edu%7C4e4c8f03c9024a45e5e508dbaf2f2b30%7C563337caa517421aaae01aa5b414fd7f%7C0%7C0%7C638296389635860385%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=0KQqptEJnoV7dGvWR3%2Be9%2Fq5gmkgy4rpjkUCzEVFxws%3D&reserved=0. (It's quite a long list, so I recommend searching for the GCF IDs directly.)

>
> I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu<mailto: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<mailto:genom...@soe.ucsc.edu>.
> ---
>
> Matthew Speir
>
> UCSC Genome Browser, User Support
>

Demayo, James

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Sep 7, 2023, 6:24:13 PM9/7/23
to Hiram Clawson, Matthew Speir, gen...@soe.ucsc.edu
Dear Matthew and Hiram,

I have been trying to work with the chain files you generated and the gtf files for the relevant assemblies with the liftOver function for downstream identification of orthologous genes (using XSAnno: https://hbatlas.org/xsanno/). I realize that the liftOver documentation suggests that the program isn't designed to lift two assemblies from two separate organisms. I am able to get results using the web browser with two separate organisms, but the command line version produces the following errors: Deleted in new:    Sequence intersects no chainsPartially deleted in new:    Sequence insufficiently intersects one chainSplit in new:    Sequence insufficiently intersects multiple chainsDuplicated in new:    Sequence sufficiently intersects multiple chainsBoundary problem:    Missing start or end base in an exon

I tried using the following options which I thought might improve the lifting, but was not successful: -multiple -minBlocks=0.9 -fudgeThick

If you have any suggestions for how to lift the two assemblies onto each other, or any other approaches I can use to identify orthologous genes between these two assemblies, I would really appreciate it.

Sincerely,

Jimmy deMayo, PhD (he/him)

Postdoctoral Researcher
Ragland lab
University of Colorado Denver
From: Demayo, James <JAMES....@UCDENVER.EDU>
Sent: Wednesday, September 6, 2023 5:29 PM
To: Hiram Clawson <hi...@soe.ucsc.edu>; Matthew Speir <msp...@ucsc.edu>

Jairo Navarro Gonzalez

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Sep 7, 2023, 7:07:58 PM9/7/23
to Demayo, James, Hiram Clawson, Matthew Speir, gen...@soe.ucsc.edu

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

To help with your issues running the liftOver program, could you send us the command you are running, along with an example of the input file?

Regarding the parameters, we used those LASTZ parameters as they tend to produce higher-quality results between similar species. You can learn more about the lastz parameters we use on the following wiki pages:

http://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl#lastz_parameter_file
http://genomewiki.ucsc.edu/index.php/Lastz_DEF_file_parameters

You can also review the following makedocs for some example dm6 LASTZ runs. Keep in mind that these makedocs are intended for internal replication.

droAna3-dm6:
https://github.com/ucscGenomeBrowser/kent/blob/7e690f333eb9b803b3a6fcceed6a404f3fdf2fb7/src/hg/makeDb/doc/dm6.txt#L798

anoGam3-dm6:
https://github.com/ucscGenomeBrowser/kent/blob/7e690f333eb9b803b3a6fcceed6a404f3fdf2fb7/src/hg/makeDb/doc/dm6.txt#L3700

A more detailed explanation of the LASTZ program can be found in the program's user guide:

https://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.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.

Jairo Navarro
UCSC Genome Browser


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Demayo, James

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Sep 8, 2023, 12:36:45 PM9/8/23
to Jairo Navarro Gonzalez, Hiram Clawson, Matthew Speir, gen...@soe.ucsc.edu
Hello Jairo,

The specific command I was running was: 

liftOver $oldFile DpersToDbipec.over.chain $newFile -multiple -minBlocks=0.9 -fudgeThick -errorHelp

where $oldFile is GCF_003286085.1_DperRS2_genomic.gtf, $newFile is GCF_018153845.1_ASM1815384v1_genomic.gtf, and DpersToDbipec.over.chain is https://hgdownload.soe.ucsc.edu/hubs/GCF/003/286/085/GCF_003286085.1/liftOver/GCF_003286085.1ToGCF_018153845.1.over.chain. All of these are unzipped before running the command.


Sincerely,

Jimmy deMayo, PhD (he/him)

Postdoctoral Researcher
Ragland lab
University of Colorado Denver
From: Jairo Navarro Gonzalez <jnav...@ucsc.edu>
Sent: Thursday, September 7, 2023 5:07 PM
To: Demayo, James <JAMES....@UCDENVER.EDU>
Cc: Hiram Clawson <hi...@soe.ucsc.edu>; Matthew Speir <msp...@ucsc.edu>; gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>

Demayo, James

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Sep 11, 2023, 6:32:39 PM9/11/23
to Jairo Navarro Gonzalez, Hiram Clawson, Matthew Speir, gen...@soe.ucsc.edu
Hi Jairo,

Does this command seem reasonable? Or am I missing something with using liftOver?

Sincerely,

Jimmy deMayo, PhD (he/him)

Postdoctoral Researcher
Ragland lab
University of Colorado Denver
From: Demayo, James <JAMES....@UCDENVER.EDU>
Sent: Friday, September 8, 2023 9:07 AM
To: Jairo Navarro Gonzalez <jnav...@ucsc.edu>

Luis Nassar

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Sep 11, 2023, 8:03:33 PM9/11/23
to Demayo, James, Jairo Navarro Gonzalez, Hiram Clawson, Matthew Speir, gen...@soe.ucsc.edu

Hello, James.

LiftOver often requires tweaking, and no parameter is really universal between even same-species organisms.

Your command looks reasonable, with the one parameter you may want to tweak being "-minBlocks=0.9". That is fairly restrictive, and fruitflies often have large amounts of diversity compared to even each other.

You could try reducing that to even as low as "-minBlocks=0.0001" in order to find lifting coordinates.

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute


Demayo, James

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Sep 12, 2023, 12:21:18 PM9/12/23
to Luis Nassar, Jairo Navarro Gonzalez, Hiram Clawson, Matthew Speir, gen...@soe.ucsc.edu
Hi Lou and other UCSC Genome folks,

Unfortunately, changing the minBlocks option yields the same error messages. Any suggestions?

Sincerely,

Jimmy deMayo, PhD (he/him)

Postdoctoral Researcher
Ragland lab
University of Colorado Denver
From: Luis Nassar <lrna...@ucsc.edu>
Sent: Monday, September 11, 2023 6:02 PM
To: Demayo, James <JAMES....@UCDENVER.EDU>
Cc: Jairo Navarro Gonzalez <jnav...@ucsc.edu>; Hiram Clawson <hi...@soe.ucsc.edu>; Matthew Speir <msp...@ucsc.edu>; gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>

Matthew Speir

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Sep 12, 2023, 6:26:35 PM9/12/23
to Demayo, James, Luis Nassar, Jairo Navarro Gonzalez, Hiram Clawson, gen...@soe.ucsc.edu
Hello, Jimmy. 

Can you try removing the "-errorHelp" option from your liftOver command? That option is used to output an explanation of all the error messages you may see in your output file and actually prevents the program from doing the lift.

Thank you!
---

Matthew Speir

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

Revealing life’s code.


Demayo, James

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Sep 12, 2023, 6:46:00 PM9/12/23
to Matthew Speir, Luis Nassar, Jairo Navarro Gonzalez, Hiram Clawson, gen...@soe.ucsc.edu
Hi Matthew,

I tried that. The only thing that happens is that the help screen with options descriptions pops up. Not sure if it's something to do with how the command is being executed or if it's missing something. What is the "unmapped" file supposed to be? I don't have that included in my command.

Sincerely,

Jimmy deMayo, PhD (he/him)

Postdoctoral Researcher
Ragland lab
University of Colorado Denver
From: Matthew Speir <msp...@ucsc.edu>
Sent: Tuesday, September 12, 2023 4:26 PM
To: Demayo, James <JAMES....@UCDENVER.EDU>
Cc: Luis Nassar <lrna...@ucsc.edu>; Jairo Navarro Gonzalez <jnav...@ucsc.edu>; Hiram Clawson <hi...@soe.ucsc.edu>; gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>

Matthew Speir

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Sep 12, 2023, 6:55:27 PM9/12/23
to Demayo, James, Luis Nassar, Jairo Navarro Gonzalez, Hiram Clawson, gen...@soe.ucsc.edu
Hi, Jimmy. 

It's a file where any items that can't be mapped between the genomes are placed, and where you'll see items with the error messages from the "-errorHelp" setting. It's a required argument to LiftOver. 

Can you try adding something like "unmapped.bed" just after $newFile in the liftOver command you shared?

Thanks!
---

Matthew Speir

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

Revealing life’s code.


Matthew Speir

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Sep 12, 2023, 7:12:52 PM9/12/23
to Demayo, James, Luis Nassar, Jairo Navarro Gonzalez, Hiram Clawson, gen...@soe.ucsc.edu
Hi, Jimmy. 

You don't need to make the file. You just need to specify a file name in your liftOver command. Your command should look like this after including this unmapped file argument:

liftOver $oldFile DpersToDbipec.over.chain $newFile unmapped.bed -multiple -minBlocks=0.01 -fudgeThick 

If there are any items that can't be mapped, liftOver will create the file "unmapped.bed" and put those unmappable items in there alongside an error message as to why they couldn't be mapped.

Thanks!
---

Matthew Speir

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

Revealing life’s code.



On Tue, Sep 12, 2023 at 4:05 PM Demayo, James <JAMES....@ucdenver.edu> wrote:
Hi Matthew,

So, just make an empty file?

Jimmy deMayo, PhD (he/him)

Postdoctoral Researcher
Ragland lab
University of Colorado Denver 
From: Matthew Speir <msp...@ucsc.edu>
Sent: Tuesday, September 12, 2023 4:55:08 PM

Demayo, James

unread,
Sep 12, 2023, 7:21:02 PM9/12/23
to Matthew Speir, Luis Nassar, Jairo Navarro Gonzalez, Hiram Clawson, gen...@soe.ucsc.edu
Hi Matthew,

So, just make an empty file?

Jimmy deMayo, PhD (he/him)

Postdoctoral Researcher
Ragland lab
University of Colorado Denver 
From: Matthew Speir <msp...@ucsc.edu>
Sent: Tuesday, September 12, 2023 4:55:08 PM

Demayo, James

unread,
Sep 12, 2023, 7:45:26 PM9/12/23
to Matthew Speir, Luis Nassar, Jairo Navarro Gonzalez, Hiram Clawson, gen...@soe.ucsc.edu
Hi Matt,

Thanks so much - that seemed to work. There only seems to be the unmapped.bed file that was created. Other than the unmapped.bed file, what output is expected, if any?

Sincerely,

Jimmy deMayo, PhD (he/him)

Postdoctoral Researcher
Ragland lab
University of Colorado Denver
From: Matthew Speir <msp...@ucsc.edu>
Sent: Tuesday, September 12, 2023 5:12 PM

Demayo, James

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Sep 13, 2023, 3:01:06 PM9/13/23
to Matthew Speir, Luis Nassar, Jairo Navarro Gonzalez, Hiram Clawson, gen...@soe.ucsc.edu
Hi Matthew,

Apologies, I now see the outputs. Thanks for your help.

Sincerely,

Jimmy deMayo, PhD (he/him)

Postdoctoral Researcher
Ragland lab
University of Colorado Denver
From: Demayo, James <JAMES....@UCDENVER.EDU>
Sent: Tuesday, September 12, 2023 5:44 PM
To: Matthew Speir <msp...@ucsc.edu>
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