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lilit-nersisyan / computel

Compute mean telomere length from Whole Genome Sequencing data.
http://big.sci.am/software/computel/
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Do fastq files need quality control before calculating telomere length? #6

Closed Captain-Pam closed 2 years ago

Captain-Pam commented 2 years ago

Hi, thank you for your research and your tool. I have fastq files with high sequencing depth, do fastq files need quality control before calculating telomere length? What quality control, if any, should be done? The default length of read is 150, do I need to change it?

Telomere length in esophageal cancer patients was estimate to be 5000-6500 using Cumputel, is this result strange?

lilit-nersisyan commented 2 years ago

Dear user,

Performing quality control increases the accuracy of measurements, particularly adapter removal. In the latest version of Computel (>1.2), the length of the reads is determined automatically based on the input files.

According to our observations, the length of telomeres in cancers as measured by Computel, usually varies in the range of 1-15kb, depending on the cancer type. So what you have observed for your esophageal cancer samples seems reasonable.

With kind regards, Lilit

On Wed, Mar 9, 2022 at 10:41 AM Pam @.***> wrote:

Hi, thank you for your research and your tool. I have fastq files with high sequencing depth, do fastq files need quality control before calculating telomere length? What quality control, if any, should be done? The default length of read is 150, do I need to change it?

Telomere length in esophageal cancer patients was estimate to be 5000-6500 using Cumputel, is this result strange?

— Reply to this email directly, view it on GitHub https://github.com/lilit-nersisyan/computel/issues/6, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZ4Y4JWOI2PRRLFPDGE3KTU7BBXXANCNFSM5QITJVVQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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-- Lilit Nersisyan, PhD Founding Director, Armenian Bioinformatics Institute Researcher, Karolinska Institutet, SciLifeLab

Captain-Pam commented 1 year ago

Hi,      Thank you for your tool. I also have a strange question, do I need to remove the sex chromosomes to estimate telomere length? IF I would like to do a GWAS analysis of telomere length.

------------------ 原始邮件 ------------------ 发件人: "lilit-nersisyan/computel" @.>; 发送时间: 2022年3月10日(星期四) 下午5:40 @.>; @.**@.>; 主题: Re: [lilit-nersisyan/computel] Do fastq files need quality control before calculating telomere length? (Issue #6)

Dear user,

Performing quality control increases the accuracy of measurements, particularly adapter removal. In the latest version of Computel (>1.2), the length of the reads is determined automatically based on the input files.

According to our observations, the length of telomeres in cancers as measured by Computel, usually varies in the range of 1-15kb, depending on the cancer type. So what you have observed for your esophageal cancer samples seems reasonable.

With kind regards, Lilit

On Wed, Mar 9, 2022 at 10:41 AM Pam @.***> wrote:

> Hi, thank you for your research and your tool. > I have fastq files with high sequencing depth, do fastq files need quality > control before calculating telomere length? What quality control, if any, > should be done? > The default length of read is 150, do I need to change it? > > Telomere length in esophageal cancer patients was estimate to be 5000-6500 > using Cumputel, is this result strange? > > — > Reply to this email directly, view it on GitHub > <https://github.com/lilit-nersisyan/computel/issues/6&gt;, or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ABZ4Y4JWOI2PRRLFPDGE3KTU7BBXXANCNFSM5QITJVVQ&gt; > . > Triage notifications on the go with GitHub Mobile for iOS > <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&amp;mt=8&amp;pt=524675&gt; > or Android > <https://play.google.com/store/apps/details?id=com.github.android&amp;referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub&gt;. > > You are receiving this because you are subscribed to this thread.Message > ID: @.***> >

-- Lilit Nersisyan, PhD Founding Director, Armenian Bioinformatics Institute Researcher, Karolinska Institutet, SciLifeLab

— Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you authored the thread.Message ID: @.***>

lilit-nersisyan commented 1 year ago

Hi,

The telomere length estimation assumes 23 pairs of chromosomes, as it doesn't distinguish between chromosomal sources of telomeric sequences, and divides the estimated total telomere length to the number of chromosome ends to derive the mean telomere length (MTL). The downstream GWAS analysis can be performed similar to any quantitative trait association study, with or without the sex chromosomes. You may refer to two of our papers for reference [ https://doi.org/10.1038/s41598-019-55109-7, https://doi.org/10.1093/bioinformatics/btw027 ].

Hope this helps, With kind regards, Lilit

On Wed, Jul 19, 2023 at 5:19 PM Pam @.***> wrote:

Hi,      Thank you for your tool. I also have a strange question, do I need to remove the sex chromosomes to estimate telomere length? IF I would like to do a GWAS analysis of telomere length.

------------------ 原始邮件 ------------------ 发件人: "lilit-nersisyan/computel" @.>; 发送时间: 2022年3月10日(星期四) 下午5:40 @.>; @.**@.>; 主题: Re: [lilit-nersisyan/computel] Do fastq files need quality control before calculating telomere length? (Issue #6)

Dear user,

Performing quality control increases the accuracy of measurements, particularly adapter removal. In the latest version of Computel (>1.2), the length of the reads is determined automatically based on the input files.

According to our observations, the length of telomeres in cancers as measured by Computel, usually varies in the range of 1-15kb, depending on the cancer type. So what you have observed for your esophageal cancer samples seems reasonable.

With kind regards, Lilit

On Wed, Mar 9, 2022 at 10:41 AM Pam @.***> wrote:

> Hi, thank you for your research and your tool. > I have fastq files with high sequencing depth, do fastq files need quality > control before calculating telomere length? What quality control, if any, > should be done? > The default length of read is 150, do I need to change it? > > Telomere length in esophageal cancer patients was estimate to be 5000-6500 > using Cumputel, is this result strange? > > — > Reply to this email directly, view it on GitHub > <https://github.com/lilit-nersisyan/computel/issues/6&gt;, or unsubscribe > < https://github.com/notifications/unsubscribe-auth/ABZ4Y4JWOI2PRRLFPDGE3KTU7BBXXANCNFSM5QITJVVQ&gt;

> . > Triage notifications on the go with GitHub Mobile for iOS > < https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&amp;mt=8&amp;pt=524675&gt;

> or Android > < https://play.google.com/store/apps/details?id=com.github.android&amp;referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub&gt;.

> > You are receiving this because you are subscribed to this thread.Message > ID: @.***> >

-- Lilit Nersisyan, PhD Founding Director, Armenian Bioinformatics Institute Researcher, Karolinska Institutet, SciLifeLab

— Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you authored the thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/lilit-nersisyan/computel/issues/6#issuecomment-1642070070, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZ4Y4L5WHGBDJZNW5EJRWTXQ7NHXANCNFSM5QITJVVQ . You are receiving this because you commented.Message ID: @.***>

-- Lilit Nersisyan, PhD Founding Director, Armenian Bioinformatics Institute Researcher, Karolinska Institutet, SciLifeLab