SK1 genome sequence

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Berchowitz Lab

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Sep 1, 2017, 1:36:53 PM9/1/17
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Hello-

My name is Luke Berchowitz and I am an assistant professor at Columbia University Medical Center. 

We recently did an experiment in which we purified an RNA-binding protein from S. cerevisiae (SK1 strain) and sequenced the associated RNA. I need to map the reads and the reference genome available on yeastgenome.org is faulty. I have noticed that IGV has a fully annotated SK1 sequence option. 

Would it be possible for you to share with me the SK1 reference files so that I can map our reads and then view them on IGV? We would greatly appreciate it.

Thanks and best regards,
Luke 

James Robinson

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Sep 1, 2017, 3:57:49 PM9/1/17
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Hi,

Unfortunately I don't have an sk1 fasta file,  this genome is an early addition to IGV and at the time we used a non-standard format.  You should be able to download the sequence as a fasta from here:  https://www.yeastgenome.org/strain/SK1



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James Robinson

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Sep 1, 2017, 4:01:05 PM9/1/17
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More specifically here:  https://downloads.yeastgenome.org/sequence/strains/SK1/SK1_SGD_2015_JRIH00000000/

Genome (fasta)

Annotations:

You will need to gunzip the fasta before loading into IGV.  Then use  "Genomes > Load genome from file".  After its loaded you can load the annotations directly from "File > Load from file"

Berchowitz Lab

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Sep 1, 2017, 4:26:30 PM9/1/17
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Hi Jim-

Thanks so much for your response. Unfortunately I have tried that and those files are incomplete and also the annotations do not work. This was why I contacted you. I have contacted SGD and have had no response so far. I will do what I can to try and find the files.

Best regards,
Luke



On Friday, September 1, 2017 at 4:01:05 PM UTC-4, Jim Robinson wrote:
More specifically here:  https://downloads.yeastgenome.org/sequence/strains/SK1/SK1_SGD_2015_JRIH00000000/

Genome (fasta)

Annotations:

You will need to gunzip the fasta before loading into IGV.  Then use  "Genomes > Load genome from file".  After its loaded you can load the annotations directly from "File > Load from file"

On Fri, Sep 1, 2017 at 3:57 PM, James Robinson <jrob...@broadinstitute.org> wrote:
Hi,

Unfortunately I don't have an sk1 fasta file,  this genome is an early addition to IGV and at the time we used a non-standard format.  You should be able to download the sequence as a fasta from here:  https://www.yeastgenome.org/strain/SK1


On Fri, Sep 1, 2017 at 1:36 PM, Berchowitz Lab <bercho...@gmail.com> wrote:
Hello-

My name is Luke Berchowitz and I am an assistant professor at Columbia University Medical Center. 

We recently did an experiment in which we purified an RNA-binding protein from S. cerevisiae (SK1 strain) and sequenced the associated RNA. I need to map the reads and the reference genome available on yeastgenome.org is faulty. I have noticed that IGV has a fully annotated SK1 sequence option. 

Would it be possible for you to share with me the SK1 reference files so that I can map our reads and then view them on IGV? We would greatly appreciate it.

Thanks and best regards,
Luke 

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James Robinson

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Sep 1, 2017, 4:30:30 PM9/1/17
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Its possible the sequence is the same as IGV uses,  so you could (possibly) use that sequence to align and then load it into IGV.  You'll know right away if its not as your alignments will all light up with mismatches.

I am attaching the gff file IGV uses. Its the fasta I don't have.



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sk1.gff3.gz

Berchowitz Lab

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Sep 1, 2017, 4:36:50 PM9/1/17
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Hi Jim-

Thanks again. I just tried the file you sent and I think it's the genome sequence that's the problem. The fasta file seems to only be ~100 kb of sequence and the SK1 genome is ~12 mb. No chromosomes are visible, only what appear to be contigs. Any help would be greatly appreciated but I understand that this probably isn't an IGV issue. 

Best regards,
Luke

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James Robinson

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Sep 1, 2017, 4:52:42 PM9/1/17
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I can create a fasts from the files we have,  but it will be next week before I can get to it.


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Berchowitz Lab

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Sep 1, 2017, 6:26:38 PM9/1/17
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Hi Jim-

Thanks a lot- that would be great. 

Have a great weekend-

Luke



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James Robinson

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Sep 5, 2017, 4:43:48 PM9/5/17
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Try this

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sk1.zip

James Robinson

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Sep 5, 2017, 4:43:49 PM9/5/17
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Try this

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sk1.zip

Berchowitz Lab

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Sep 6, 2017, 6:02:04 PM9/6/17
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Thanks so much Jim! I'll try it and let you know.

Best regards,
Luke
Try this

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elze...@gmail.com

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Jul 5, 2019, 1:09:49 PM7/5/19
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Hi James,
Just wonde if you have a proper gff3/gtf annotation for SK1 with gene_ID and transcript_ID information?
Thanks a lot.
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