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icthrm / cwSDTWnano

Here we proposed two novel algorithms, the Direct Subsequence Dynamic Time Warping for nanopore raw signal search (DSDTWnano) and the continuous wavelet Subsequence DTW for nanopore raw signal search (cwSDTWnano), to enable the direct subsequence inquiry and exact mapping in the nanopore raw signal datasets. The proposed algorithms are based on the idea of Subsequence-extended Dynamic Time Warping (SDTW) and directly operates on the raw signals, without any loss of information. DSDTWnano could ensure an output of highly accurate query result and cwSDTWnano is the accelerated version of DSDTWnano, with the help of seeding and multi-scale coarsening of signals that based on continuous wavelet transform (CWT).
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Does methlyation state influence expected signal? #2

Open PanZiwei opened 4 years ago

PanZiwei commented 4 years ago

Hi,

I have a question about your algorithm usage.

Your algorithm is a signal-based approach. When you translate the genomic region of interest into the expected signals by the k-mer pore model, does the methylation state influence the expected signals? Since Laszlo et al have shown that DNA modification will affect the shape and mode of the current, did you evaluate your model on the dataset with DNA modifications?

Thank you so much for your help!

icthrm commented 4 years ago

Dear Ziwei,

The methylation will change the signals. However, for mapping purposes, we still can use the non-methylated expected signal to find the interesting raw reads by clustering.

Yours,

Renmin Han

PanZiwei notifications@github.com 于2020年6月5日周五 上午11:00写道：

Hi,

I have a question about your algorithm usage.

Your algorithm is a signal-based approach. When you translate the genomic region of interest into the expected signals by the k-mer pore model, does the methylation state influence the expected signals? Since Laszlo et al https://www.pnas.org/content/110/47/18904 have shown that DNA modification will affect the shape and mode of the current, did you evaluate your model on the dataset with DNA modifications?

Thank you so much for your help!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/icthrm/cwSDTWnano/issues/2, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB2IPE3OHVBHX23J2UKN5UTRVBNU5ANCNFSM4NTFHPDQ .

PanZiwei commented 4 years ago

Dear Ziwei, The methylation will change the signals. However, for mapping purposes, we still can use the non-methylated expected signal to find the interesting raw reads by clustering. Yours, Renmin Han PanZiwei notifications@github.com 于2020年6月5日周五 上午11:00写道： … Hi, I have a question about your algorithm usage. Your algorithm is a signal-based approach. When you translate the genomic region of interest into the expected signals by the k-mer pore model, does the methylation state influence the expected signals? Since Laszlo et al https://www.pnas.org/content/110/47/18904 have shown that DNA modification will affect the shape and mode of the current, did you evaluate your model on the dataset with DNA modifications? Thank you so much for your help! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB2IPE3OHVBHX23J2UKN5UTRVBNU5ANCNFSM4NTFHPDQ .

Hi Renmin, Thank you so much for your reply!

Just have several following questions:

  1. What is your output format actually?.sam/.tsv/.bed? Is the mapping output applicable to available methylation calling software to call methylation states? How can I use the results of mapping from your signal-based approach to detect methylation states?

  2. Do you have a pipeline for methylation calling if I want to use your signal-based approach?

For your reference, I summary the general pipeline for the methylation calling in read-to-reference approach below: Nanopore sequencing(.fast5) + genome(.fasta) -> Base-calling(e.g. Guppy) for .fastq -> Alignment and mapping(e.g. Minimap2) -> Methylation calling with specific software(e.g. Nanopolish-require .tsv input, Tombo-require .bed input)

  1. Do you have any plan to visualizing the mapping result of signal with genome?

Thank you so much for your help!

icthrm commented 4 years ago

Dear Ziwei,

Sorry for the late reply.

  1. You can use our painting tool to see the detailed output. We have the format details on the github. 2. We are trying to make methylation calling by our tools. However, it still takes time to release the project. 3. Are you mean to build a mapping relationship between signals and genome locations?

Yours,

Renmin Han

PanZiwei notifications@github.com 于2020年6月5日周五 下午12:14写道：

Dear Ziwei, The methylation will change the signals. However, for mapping purposes, we still can use the non-methylated expected signal to find the interesting raw reads by clustering. Yours, Renmin Han PanZiwei notifications@github.com 于2020年6月5日周五 上午11:00写道： … <#m1370882586542828382> Hi, I have a question about your algorithm usage. Your algorithm is a signal-based approach. When you translate the genomic region of interest into the expected signals by the k-mer pore model, does the methylation state influence the expected signals? Since Laszlo et al https://www.pnas.org/content/110/47/18904 have shown that DNA modification will affect the shape and mode of the current, did you evaluate your model on the dataset with DNA modifications? Thank you so much for your help! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2 https://github.com/icthrm/cwSDTWnano/issues/2>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB2IPE3OHVBHX23J2UKN5UTRVBNU5ANCNFSM4NTFHPDQ .

Hi Renmin, Thank you so much for your reply!

Just have several following questions:

1.

What is your output format actually? Is the mapping output applicable to available methylation calling software to call methylation states? How can I use the results of mapping from your signal-based approach to detect methylation states? 2.

Do you have a pipeline for methylation calling if I want to use your signal-based approach? How

For your reference, I summary the general pipeline for the methylation calling in read-to-reference approach below: Nanopore sequencing(.fast5) + genome(.fasta) -> Base-calling(e.g. Guppy) for .fastq -> Alignment and mapping(e.g. Minimap2) -> Methylation calling with specific software(e.g. Nanopolish, Tombo)

  1. Do you have any plan to visualizing the mapping result of signal with genome?

Thank you so much for your help!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/icthrm/cwSDTWnano/issues/2#issuecomment-639247520, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB2IPE2HLNOO7OOB4SXALO3RVBWJJANCNFSM4NTFHPDQ .

PanZiwei commented 4 years ago

Hi Renmin,

Thank you so much for your reply!

  1. I will have a try with your tool to see the output format as you suggest.

  2. So you are trying to developing a new algorithm to directly do the methylation calling from your signal information, instead of integrating the current tools such as Guppy released by Nanopore?

  3. For the visualization, I am talking about something like Figure 2c in the Tombo poster, which shows the signal distribution with the corresponding sequence information(maybe with modification also).