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harbourlab / SparK

Publication quality NGS track plotting
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Gene body could not be plotted correctly #4

Closed lz43771 closed 4 years ago

lz43771 commented 4 years ago

Hi,

I tried to plot ATAC-Seq and RNA-Seq data together. While the track looks great, the gene body/transcript could not be visualized correctly. The exons are plotted while all the introns are not (so there is no line connecting the exons). I tried multiple ways but the issue still remains.

I tried -dg -dt -wg. None of them solved this problem. Here is the code I used:

python SparK.py \ -pr chr8:25818128-26065154 \ -cf d0.CallPeak_treat_pileup.bdg d4.CallPeak_treat_pileup.bdg d8.CallPeak_treat_pileup.bdg \ d15.CallPeak_treat_pileup.bdg d20.CallPeak_treat_pileup.bdg d24.CallPeak_treat_pileup.bdg \ -gff hg38.ncbiRefSeq.gtf \ -gl D0 D4 D8 D15 D20 D24 \ -dg EBF2 \ -gs yes \ -o EBF2_tes1

harbourlab commented 4 years ago

Hi!

I checked with some data from me and the gene plots correctly. I believe the problem lies with the gtf file you are using. Please follow the link on the SparK site to the GENCODE site, and download the gff file for hg38 (https://www.gencodegenes.org/human/release_24.html). Also make sure to run the latest version of SparK (2.5.1). Let me know if that solves the problem for you!

Cheers, Stefan

harbourlab commented 4 years ago

I'm closing this issue, but let me know if you have any problems!

lz43771 commented 4 years ago

Hi Stefan,

Thank you for your reply and I am really appreciated for your help!

I was writing my paper and just got time to test what you suggested. I tried multiple gff3 and gtf files (gencode, NCBIrefseq, ensemble) . Currently, only the primary assemble gtf from the gencode works for me and I get the gene/transcript graphing correctly.

I noticed you wrote notification for the gff files in the Github page. All the gff3/gtf files I used seem to meet the requirement. I have no idea why they didn’t work out. I attached 2 pdf with result I got when using the same code but different gtf/gff.

Best, Brian

On May 4, 2020, at 12:33 PM, Harbour Ocular Oncology Laboratory notifications@github.com<mailto:notifications@github.com> wrote:

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

I'm closing this issue, but let me know if you have any problems!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/harbourlab/SparK/issues/4#issuecomment-623570337, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AED657NI2SBDMQL3P3MYFTDRP3U6XANCNFSM4MX54RYA.

harbourlab commented 4 years ago

Hi Brian,

I am happy that the issue has resolved! Not sure why the other files have not worked. Sop the GENCODE gff file and the GENCODE gtf file did both work? Or only one of both?

Cheers Stefan

Stefan Kurtenbach Assistant Scientist Harbour Ocular Oncology Laboratory University of Miami Miller School of Medicine Biomedical Research Building Room 832, Suite H-I 1501 NW 10th Avenue Miami, FL 33136

305-326-6020 lab 786-252-4379 cell

On May 4, 2020, at 10:47 PM, lz43771 notifications@github.com<mailto:notifications@github.com> wrote:

Hi Stefan,

Thank you for your reply and I am really appreciated for your help!

I was writing my paper and just got time to test what you suggested. I tried multiple gff3 and gtf files (gencode, NCBIrefseq, ensemble) . Currently, only the primary assemble gtf from the gencode works for me and I get the gene/transcript graphing correctly.

I noticed you wrote notification for the gff files in the Github page. All the gff3/gtf files I used seem to meet the requirement. I have no idea why they didn’t work out. I attached 2 pdf with result I got when using the same code but different gtf/gff.

Best, Brian

On May 4, 2020, at 12:33 PM, Harbour Ocular Oncology Laboratory notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

I'm closing this issue, but let me know if you have any problems!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/harbourlab/SparK/issues/4#issuecomment-623570337, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AED657NI2SBDMQL3P3MYFTDRP3U6XANCNFSM4MX54RYA.

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lz43771 commented 4 years ago

Hi Stefan,

Only the gtf worked for me. The gff3 could not generate the transcript.

Best, Brian

From: Harbour Ocular Oncology Laboratory notifications@github.com Sent: Tuesday, May 5, 2020 12:19 PM To: harbourlab/SparK SparK@noreply.github.com Cc: Liang Zhang lz43771@uga.edu; Author author@noreply.github.com Subject: Re: [harbourlab/SparK] Gene body could not be plotted correctly (#4)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Hi Brian,

I am happy that the issue has resolved! Not sure why the other files have not worked. Sop the GENCODE gff file and the GENCODE gtf file did both work? Or only one of both?

Cheers Stefan

Stefan Kurtenbach Assistant Scientist Harbour Ocular Oncology Laboratory University of Miami Miller School of Medicine Biomedical Research Building Room 832, Suite H-I 1501 NW 10th Avenue Miami, FL 33136

305-326-6020 lab 786-252-4379 cell

On May 4, 2020, at 10:47 PM, lz43771 notifications@github.com<mailto:notifications@github.com> wrote:

Hi Stefan,

Thank you for your reply and I am really appreciated for your help!

I was writing my paper and just got time to test what you suggested. I tried multiple gff3 and gtf files (gencode, NCBIrefseq, ensemble) . Currently, only the primary assemble gtf from the gencode works for me and I get the gene/transcript graphing correctly.

I noticed you wrote notification for the gff files in the Github page. All the gff3/gtf files I used seem to meet the requirement. I have no idea why they didn’t work out. I attached 2 pdf with result I got when using the same code but different gtf/gff.

Best, Brian

On May 4, 2020, at 12:33 PM, Harbour Ocular Oncology Laboratory notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

I'm closing this issue, but let me know if you have any problems!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/harbourlab/SparK/issues/4#issuecomment-623570337, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AED657NI2SBDMQL3P3MYFTDRP3U6XANCNFSM4MX54RYA.

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harbourlab commented 4 years ago

Thank you for letting me know Brian. I am not sure what changed, but seems gtf files are the only ones working now. I will make an update on the site to state this. Thanks again!

lz43771 commented 4 years ago

Hi Stefan,

May I know if your spark paper has been accepted or not? I am working my reference list and would like to add it. May I know you have any suggestion on how to cite it?

Best, Brian

On May 5, 2020, at 6:29 PM, Harbour Ocular Oncology Laboratory notifications@github.com<mailto:notifications@github.com> wrote:

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Thank you for letting me know Brian. I am not sure what changed, but seems gtf files are the only ones working now. I will make an update on the site to state this. Thanks again!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/harbourlab/SparK/issues/4#issuecomment-624340372, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AED657JOKTJVE4THYBCI4U3RQCHM3ANCNFSM4MX54RYA.

harbourlab commented 4 years ago

Hi Brian! Thank you! I have not submitted it to a peer-reviewed journal yet, but I would be grateful if you could cite the biorxiv paper!

https://www.biorxiv.org/content/10.1101/845529v1

You can download a reference there and import it in endnote or such!

Thanks again! Stefan

lz43771 commented 4 years ago

Thank you Stefan. Will do as you recommend. I really like this tool and it is really helpful!

On May 7, 2020, at 5:12 PM, Harbour Ocular Oncology Laboratory notifications@github.com<mailto:notifications@github.com> wrote:

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Hi Brian! Thank you! I have not submitted it to a peer-reviewed journal yet, but I would be grateful if you could cite the biorxiv paper!

https://www.biorxiv.org/content/10.1101/845529v1

You can download a reference there and import it in endnote or such!

Thanks again! Stefan

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/harbourlab/SparK/issues/4#issuecomment-625500273, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AED657KAFS3G2YYYJL6IWI3RQMP4LANCNFSM4MX54RYA.

harbourlab commented 4 years ago

Thank you! I am happy you find it useful! Let me know if you need anything down the road and good luck with your publication!!

Cheers Stefan

Stefan Kurtenbach Assistant Scientist Harbour Ocular Oncology Laboratory University of Miami Miller School of Medicine Biomedical Research Building Room 832, Suite H-I 1501 NW 10th Avenue Miami, FL 33136

305-326-6020 lab 786-252-4379 cell

On May 7, 2020, at 5:14 PM, lz43771 notifications@github.com<mailto:notifications@github.com> wrote:

Thank you Stefan. Will do as you recommend. I really like this tool and it is really helpful!

On May 7, 2020, at 5:12 PM, Harbour Ocular Oncology Laboratory notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Hi Brian! Thank you! I have not submitted it to a peer-reviewed journal yet, but I would be grateful if you could cite the biorxiv paper!

https://www.biorxiv.org/content/10.1101/845529v1

You can download a reference there and import it in endnote or such!

Thanks again! Stefan

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/harbourlab/SparK/issues/4#issuecomment-625500273, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AED657KAFS3G2YYYJL6IWI3RQMP4LANCNFSM4MX54RYA.

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