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salmo salar genome request #76
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Thanks for your interest. I'd love to make epic usable on less common builds/genomes, as I know that is a pain point with many other callers. All you need is a file with the chromosome/unplaced contig names in one column and the sizes in another. For UCSC this might look like:
Then you can invoke epic with The egf suggestion is just a hack until I am able to get the egf info which is computationally expensive. Do you have a link to a fasta genome of your organism? Endre |
Also, do you have input/background files? epic needs that to run - just telling you upfront so you do not waste your time :) |
Hi Endre!
Thanks a lot for your help!
I got confused because I was providing the fasta file with the option -gn
(i thought epic need it XP) ... I just removed this option, including the
chromsize_file and -egf 0.8 (indeed, this was the % of unique mapped reads
reported by bowtie2), and the program is running since this morning!!!
This is the link for the salmon's genome:
https://www.ncbi.nlm.nih.gov/genome/?term=txid8030[orgn]
(I also included the unplaced contigs because there are many gene of my
interest on this sequences)
Thanks again for your help!
Estefania
…___________________
*Estefania Tarifeño,* *PhD.*
Assistant professor
Department of Biochemistry and Molecular Biology
Faculty of Biological Sciences
University of Concepción, Concepción, Chile
(+56)(41)2203784
2018-04-12 3:02 GMT-03:00 Endre Bakken Stovner <[email protected]>:
Also, do you have input files? epic needs that to run.
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But epic should be pretty fast. If it has been running for a long time there is something strange going on :/ |
Really?
It has been printing "Making duplicated bins unique by summing them. (File:
count_reads_in_windows, Log level: INFO, Time: Fri, 13 Apr 2018 09:09:52 )"
since yesterday.
This is my script:
---------------------------------
epic \
--treatment infected_A1.bedpe \
--control control_A1.bedpe \
--number-cores 6 \
-egf 0.8 \
--window-size 200 --gaps-allowed 3 \
--chromsizes ssa_ref_ICSASG_v2_rename_size.genome \
--bed condition_A.bed \
--outfile condition_A.csv
---------------------------------
Is there any mistake?
Thanks for your help!
Estefanía
…___________________
*Estefania Tarifeño,* *PhD.*
Assistant professor
Department of Biochemistry and Molecular Biology
Faculty of Biological Sciences
University of Concepción, Concepción, Chile
(+56)(41)2203784
2018-04-13 3:55 GMT-03:00 Endre Bakken Stovner <[email protected]>:
But epic should be pretty fast. If it has been running for a long time
there is something strange going on :/
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or mute the thread
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Are you able to share the files with me? Then I could debug easily. Dropbox
link to endrebak85 gmail.com would work.
…On Fri, Apr 13, 2018 at 2:15 PM, etarisal ***@***.***> wrote:
Really?
It has been printing "Making duplicated bins unique by summing them. (File:
count_reads_in_windows, Log level: INFO, Time: Fri, 13 Apr 2018 09:09:52 )"
since yesterday.
This is my script:
---------------------------------
epic \
--treatment infected_A1.bedpe \
--control control_A1.bedpe \
--number-cores 6 \
-egf 0.8 \
--window-size 200 --gaps-allowed 3 \
--chromsizes ssa_ref_ICSASG_v2_rename_size.genome \
--bed condition_A.bed \
--outfile condition_A.csv
---------------------------------
Is there any mistake?
Thanks for your help!
Estefanía
___________________
*Estefania Tarifeño,* *PhD.*
Assistant professor
Department of Biochemistry and Molecular Biology
Faculty of Biological Sciences
University of Concepción, Concepción, Chile
(+56)(41)2203784
2018-04-13 3:55 GMT-03:00 Endre Bakken Stovner ***@***.***>:
> But epic should be pretty fast. If it has been running for a long time
> there is something strange going on :/
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <#76 (comment)>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AkhqHX6AtuCqn_
6vHmziXNFj0xLrMjeiks5toEvygaJpZM4TQzU_>
> .
>
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|
Sure!!!
Thank you!
I got my Dropbox full, but it should work with this google drive link.
https://drive.google.com/drive/folders/17e-93XamXzhJPbtRTo1un-UZLCuyNHdp?usp=sharing
I uploaded a control and a treatment bedpe file, and also my
chromosome_size file (with unplaced contigs)
Let me know if you need any other information...
Thanks again for your help!
:D
Estefanía
…___________________
*Estefania Tarifeño,* *PhD.*
Assistant professor
Department of Biochemistry and Molecular Biology
Faculty of Biological Sciences
University of Concepción, Concepción, Chile
(+56)(41)2203784
2018-04-13 11:06 GMT-03:00 Endre Bakken Stovner <[email protected]>:
Are you able to share the files with me? Then I could debug easily. Dropbox
link to endrebak85 gmail.com would work.
On Fri, Apr 13, 2018 at 2:15 PM, etarisal ***@***.***>
wrote:
> Really?
>
> It has been printing "Making duplicated bins unique by summing them.
(File:
> count_reads_in_windows, Log level: INFO, Time: Fri, 13 Apr 2018 09:09:52
)"
> since yesterday.
>
>
> This is my script:
> ---------------------------------
> epic \
> --treatment infected_A1.bedpe \
> --control control_A1.bedpe \
> --number-cores 6 \
> -egf 0.8 \
> --window-size 200 --gaps-allowed 3 \
> --chromsizes ssa_ref_ICSASG_v2_rename_size.genome \
> --bed condition_A.bed \
> --outfile condition_A.csv
> ---------------------------------
>
> Is there any mistake?
>
> Thanks for your help!
>
> Estefanía
>
>
> ___________________
> *Estefania Tarifeño,* *PhD.*
> Assistant professor
> Department of Biochemistry and Molecular Biology
> Faculty of Biological Sciences
> University of Concepción, Concepción, Chile
> (+56)(41)2203784
>
>
>
> 2018-04-13 3:55 GMT-03:00 Endre Bakken Stovner ***@***.***
>:
>
> > But epic should be pretty fast. If it has been running for a long time
> > there is something strange going on :/
> >
> > —
> > You are receiving this because you authored the thread.
> > Reply to this email directly, view it on GitHub
> > <#76 (comment)
>,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/AkhqHX6AtuCqn_
> 6vHmziXNFj0xLrMjeiks5toEvygaJpZM4TQzU_>
> > .
> >
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <#76 (comment)>,
> or mute the thread
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Y4kGwEnLikme60Qi3pFks5toJbOgaJpZM4TQzU_>
> .
>
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|
Thanks. I haven’t tried it on assemblies/contigs before.
Endre
…On Friday, April 13, 2018, etarisal ***@***.***> wrote:
Sure!!!
Thank you!
I got my Dropbox full, but it should work with this google drive link.
https://drive.google.com/drive/folders/17e-93XamXzhJPbtRTo1un-UZLCuyNHdp?
usp=sharing
I uploaded a control and a treatment bedpe file, and also my
chromosome_size file (with unplaced contigs)
Let me know if you need any other information...
Thanks again for your help!
:D
Estefanía
___________________
*Estefania Tarifeño,* *PhD.*
Assistant professor
Department of Biochemistry and Molecular Biology
Faculty of Biological Sciences
University of Concepción, Concepción, Chile
(+56)(41)2203784
2018-04-13 11:06 GMT-03:00 Endre Bakken Stovner ***@***.***
>:
> Are you able to share the files with me? Then I could debug easily.
Dropbox
> link to endrebak85 gmail.com would work.
>
> On Fri, Apr 13, 2018 at 2:15 PM, etarisal ***@***.***>
> wrote:
>
> > Really?
> >
> > It has been printing "Making duplicated bins unique by summing them.
> (File:
> > count_reads_in_windows, Log level: INFO, Time: Fri, 13 Apr 2018
09:09:52
> )"
> > since yesterday.
> >
> >
> > This is my script:
> > ---------------------------------
> > epic \
> > --treatment infected_A1.bedpe \
> > --control control_A1.bedpe \
> > --number-cores 6 \
> > -egf 0.8 \
> > --window-size 200 --gaps-allowed 3 \
> > --chromsizes ssa_ref_ICSASG_v2_rename_size.genome \
> > --bed condition_A.bed \
> > --outfile condition_A.csv
> > ---------------------------------
> >
> > Is there any mistake?
> >
> > Thanks for your help!
> >
> > Estefanía
> >
> >
> > ___________________
> > *Estefania Tarifeño,* *PhD.*
> > Assistant professor
> > Department of Biochemistry and Molecular Biology
> > Faculty of Biological Sciences
> > University of Concepción, Concepción, Chile
> > (+56)(41)2203784
> >
> >
> >
> > 2018-04-13 3:55 GMT-03:00 Endre Bakken Stovner <
***@***.***
> >:
> >
> > > But epic should be pretty fast. If it has been running for a long
time
> > > there is something strange going on :/
> > >
> > > —
> > > You are receiving this because you authored the thread.
> > > Reply to this email directly, view it on GitHub
> > > <#76#
issuecomment-381042227
> >,
> > > or mute the thread
> > > <https://github.com/notifications/unsubscribe-auth/AkhqHX6AtuCqn_
> > 6vHmziXNFj0xLrMjeiks5toEvygaJpZM4TQzU_>
> > > .
> > >
> >
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub
> > <#76 (comment)
>,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/AQ9I0oNGBbAi_
> Y4kGwEnLikme60Qi3pFks5toJbOgaJpZM4TQzU_>
> > .
>
> >
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <#76 (comment)>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AkhqHac3BuJDEo56E_
lyfZ1a5luYFQVkks5toLDQgaJpZM4TQzU_>
> .
>
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Ok!, maybe is the reason why is taking so long...
I see that epic is at least calculating (something) and taking about 2-4
cores depending on the time I check (using top)
I am running the same dataset on my computer...But let me know if you have
any suggestion to speed up the run!
Thank you!
Estefanía
…___________________
*Estefania Tarifeño,* *PhD.*
Assistant professor
Department of Biochemistry and Molecular Biology
Faculty of Biological Sciences
University of Concepción, Concepción, Chile
(+56)(41)2203784
2018-04-13 13:44 GMT-03:00 Endre Bakken Stovner <[email protected]>:
Thanks. I haven’t tried it on assemblies/contigs before.
Endre
On Friday, April 13, 2018, etarisal ***@***.***> wrote:
> Sure!!!
> Thank you!
>
> I got my Dropbox full, but it should work with this google drive link.
> https://drive.google.com/drive/folders/17e-93XamXzhJPbtRTo1un-UZLCuyNHdp
?
> usp=sharing
>
> I uploaded a control and a treatment bedpe file, and also my
> chromosome_size file (with unplaced contigs)
> Let me know if you need any other information...
>
> Thanks again for your help!
> :D
> Estefanía
>
>
> ___________________
> *Estefania Tarifeño,* *PhD.*
> Assistant professor
> Department of Biochemistry and Molecular Biology
> Faculty of Biological Sciences
> University of Concepción, Concepción, Chile
> (+56)(41)2203784
>
>
>
> 2018-04-13 11:06 GMT-03:00 Endre Bakken Stovner <
***@***.***
> >:
>
> > Are you able to share the files with me? Then I could debug easily.
> Dropbox
> > link to endrebak85 gmail.com would work.
> >
> > On Fri, Apr 13, 2018 at 2:15 PM, etarisal ***@***.***>
> > wrote:
> >
> > > Really?
> > >
> > > It has been printing "Making duplicated bins unique by summing them.
> > (File:
> > > count_reads_in_windows, Log level: INFO, Time: Fri, 13 Apr 2018
> 09:09:52
> > )"
> > > since yesterday.
> > >
> > >
> > > This is my script:
> > > ---------------------------------
> > > epic \
> > > --treatment infected_A1.bedpe \
> > > --control control_A1.bedpe \
> > > --number-cores 6 \
> > > -egf 0.8 \
> > > --window-size 200 --gaps-allowed 3 \
> > > --chromsizes ssa_ref_ICSASG_v2_rename_size.genome \
> > > --bed condition_A.bed \
> > > --outfile condition_A.csv
> > > ---------------------------------
> > >
> > > Is there any mistake?
> > >
> > > Thanks for your help!
> > >
> > > Estefanía
> > >
> > >
> > > ___________________
> > > *Estefania Tarifeño,* *PhD.*
> > > Assistant professor
> > > Department of Biochemistry and Molecular Biology
> > > Faculty of Biological Sciences
> > > University of Concepción, Concepción, Chile
> > > (+56)(41)2203784
> > >
> > >
> > >
> > > 2018-04-13 3:55 GMT-03:00 Endre Bakken Stovner <
> ***@***.***
> > >:
> > >
> > > > But epic should be pretty fast. If it has been running for a long
> time
> > > > there is something strange going on :/
> > > >
> > > > —
> > > > You are receiving this because you authored the thread.
> > > > Reply to this email directly, view it on GitHub
> > > > <#76#
> issuecomment-381042227
> > >,
> > > > or mute the thread
> > > > <https://github.com/notifications/unsubscribe-auth/AkhqHX6AtuCqn_
> > > 6vHmziXNFj0xLrMjeiks5toEvygaJpZM4TQzU_>
> > > > .
> > > >
> > >
> > > —
> > > You are receiving this because you commented.
> > > Reply to this email directly, view it on GitHub
> > > <#76#
issuecomment-381116960
> >,
> > > or mute the thread
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> > Y4kGwEnLikme60Qi3pFks5toJbOgaJpZM4TQzU_>
> > > .
> >
> > >
> >
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> > You are receiving this because you authored the thread.
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>,
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Hmm, usual genomes have ~25 chromosomes, with your contigs you have 232155. This might be why it takes so long. Is it possible to only run it on the canonical chromosomes? I will think more about it, I promise. |
Yep! it run smoothly using only canonical chromosomes....
I will pick up the most important scaffolds in order to reduce the number
of contigs on the annotations.
Thank you for your help,
Cheers,
Estefanía
…___________________
*Estefania Tarifeño,* *PhD.*
Assistant professor
Department of Biochemistry and Molecular Biology
Faculty of Biological Sciences
University of Concepción, Concepción, Chile
(+56)(41)2203784
2018-04-15 8:02 GMT-03:00 Endre Bakken Stovner <[email protected]>:
Hmm, usual genomes have ~25 chromosomes, with your contigs you have
232155. This might be why it takes so long. Is it possible to only run it
on the canonical chromosomes?
I will think more about it, I promise.
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Hello,
I am working with Chip-seq data (Histone modifications) from Salmo salar and I would like to ask you if it is possible to request the genome and genome size file for this organism?. Or any help to create include the annotation I used for the mapping in the epic run?
The genome annotation I used for the mapping is the one found at NCBI (https://www.ncbi.nlm.nih.gov/genome/369?genome_assembly_id=248466), I also include the "unplaced contigs" in this process.
Thanks for your help,
Cheers,
Estefania
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