TRUST for T cell receptor hypervariable region assembly

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Welcome to TRUST user group! Please post your questions related to the usage of TRUST and we will get back to you at our earliest convenience.

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yang, Jean-Baptiste Reynier2

9/16/19

The result of TRUST

Hello, I had the same question, and I was wondering if anyone had an answer. Thank you, Best, JB On

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The result of TRUST

Hello, I had the same question, and I was wondering if anyone had an answer. Thank you, Best, JB On

9/16/19

孙强

8/23/19

Trust execution error with -B -L parameters

Hi, It is ok with -B, -T option for the same bam file. However, I encountered execution error with a

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Trust execution error with -B -L parameters

Hi, It is ok with -B, -T option for the same bam file. However, I encountered execution error with a

8/23/19

Tina

8/13/19

The difference bwt TCR-ALL.txt and TCR-ALL.fa

What's the difference between TCR-ALL.txt and TCR-ALL.fa these two file? Some of them I found

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The difference bwt TCR-ALL.txt and TCR-ALL.fa

What's the difference between TCR-ALL.txt and TCR-ALL.fa these two file? Some of them I found

8/13/19

Daniel Gusenleitner

6/10/19

Estimation of BCR clonality

Hi Bo and Xiahao, your paper on the landscape of B-cell immunity recently was really interesting.

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Estimation of BCR clonality

Hi Bo and Xiahao, your paper on the landscape of B-cell immunity recently was really interesting.

6/10/19

11033...@qq.com, … Jian Zhang6

6/4/19

Installation error: command 'gcc' failed with exit status 1

Hi Kevin, Sorry for the delay response. I have some connection issues with my gmail account recently.

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Installation error: command 'gcc' failed with exit status 1

Hi Kevin, Sorry for the delay response. I have some connection issues with my gmail account recently.

6/4/19

Jean-Baptiste Reynier, … Bo Li3

5/7/19

STAR alignment criteria

Thanks a lot for the helpful discussions! Best, Bo On Tue, May 7, 2019 at 4:31 PM <zhengyonglan@

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STAR alignment criteria

Thanks a lot for the helpful discussions! Best, Bo On Tue, May 7, 2019 at 4:31 PM <zhengyonglan@

5/7/19

royalbe...@gmail.com, … Jian Zhang6

4/10/19

trust executable options

Hi Bo, I don't think we have those modules in any version of TRUST. Hi Uma, could you please try

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trust executable options

Hi Bo, I don't think we have those modules in any version of TRUST. Hi Uma, could you please try

4/10/19

venomou...@gmail.com, Bo Li2

3/5/19

version of genome database

The setting should be fine. Just specify the right genome build. On Tue, Mar 5, 2019 at 3:23 AM <

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version of genome database

The setting should be fine. Just specify the right genome build. On Tue, Mar 5, 2019 at 3:23 AM <

3/5/19

yhf....@gmail.com2

2/25/19

Quantitative measure of clonality for each TCR sequence

Hi Bo, Sorry to add, but to give my question more clarity, this is essentially what I wanted to

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Quantitative measure of clonality for each TCR sequence

Hi Bo, Sorry to add, but to give my question more clarity, this is essentially what I wanted to

2/25/19

yhf....@gmail.com, … rkanh...@gmail.com5

2/6/19

Error installing TRUST: ImportError: No module named _build_utils.apple_accelerate

Hi, I am getting same error while intalling pandas. Appreciate if I can get some solution. Thanks,

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Error installing TRUST: ImportError: No module named _build_utils.apple_accelerate

Hi, I am getting same error while intalling pandas. Appreciate if I can get some solution. Thanks,

2/6/19

yang, … zhangda...@gmail.com5

12/28/18

The inputs of TRUST

So, generally speaking, at what kind of mapping quality threshold can you get rid of multiply mapping

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The inputs of TRUST

So, generally speaking, at what kind of mapping quality threshold can you get rid of multiply mapping

12/28/18

11485...@qq.com

12/22/18

question

From where i can gat the detail information of this program

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question

From where i can gat the detail information of this program

12/22/18

tianxiao...@gmail.com, … zhang...@gmail.com4

12/4/18

Error: Please provide the correct BAM index file!

Sure, Bo! Hi Tian, can you try '-g hg38'? I think there is a missing of '-g' before

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Error: Please provide the correct BAM index file!

Sure, Bo! Hi Tian, can you try '-g hg38'? I think there is a missing of '-g' before

12/4/18

yang

11/29/18

The impact of short sequences on TRUST

Hi Bo, I am using Trim Galore software of RNA-seq data Quality control for me, has the following

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The impact of short sequences on TRUST

Hi Bo, I am using Trim Galore software of RNA-seq data Quality control for me, has the following

11/29/18

hischm...@googlemail.com, Bo Li2

11/14/18

How are 'est_clonal_exp' values calculated in TCR-ALL.txt files

Hi Paul, As you can imagine, a short piece of DNA fragment might be able to mapped to more than one

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How are 'est_clonal_exp' values calculated in TCR-ALL.txt files

Hi Paul, As you can imagine, a short piece of DNA fragment might be able to mapped to more than one

11/14/18

tianxiao...@gmail.com, Bo Li2

10/19/18

Can Whole Exome Sequencing BAM files used in the TCR/BCR analysis?

Hi Tian, We haven't tested it on WES data yet, but it completely depends on if the exome capture

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Can Whole Exome Sequencing BAM files used in the TCR/BCR analysis?

Hi Tian, We haven't tested it on WES data yet, but it completely depends on if the exome capture

10/19/18

Paul, Bo Li2

10/2/18

PE mode vs SE mode

Hi Paul, Thank you for using our method. I would recommend PE mode as long as you can run it through.

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PE mode vs SE mode

Hi Paul, Thank you for using our method. I would recommend PE mode as long as you can run it through.

10/2/18

11033...@qq.com

8/25/18

Running TRUST in PE mode

Hi Bo, When I run TRUST on my paired-end RNA-Seq data, it will change to single end mode during the

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Running TRUST in PE mode

Hi Bo, When I run TRUST on my paired-end RNA-Seq data, it will change to single end mode during the

8/25/18

me.x...@gmail.com, … Bo Li7

8/16/18

sre_constants.error: nothing to repeat

Jian, it works well after upgraded to v3.0.3. Thanks for all your help. Ying On Wed, Aug 15, 2018 at

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sre_constants.error: nothing to repeat

Jian, it works well after upgraded to v3.0.3. Thanks for all your help. Ying On Wed, Aug 15, 2018 at

8/16/18

sjtu....@gmail.com, Bo Li6

7/30/18

segmentation fault (core dumped)

How large is the unmapped.bam file? Thanks, Bo On Mon, Jul 30, 2018 at 9:10 AM, sjtu.syang <sjtu.

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segmentation fault (core dumped)

How large is the unmapped.bam file? Thanks, Bo On Mon, Jul 30, 2018 at 9:10 AM, sjtu.syang <sjtu.

7/30/18

nor...@googlegroups.com

7/18/18

申请更改 Google 网上论坛邀请设置

Google Groups Google 网上论坛徽标 trus...@googlegroups.com 帐号申请更改其 Google 网上论坛邀请设置。要确认此申请并更改选项，请使用下方的邀请设置

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申请更改 Google 网上论坛邀请设置

Google Groups Google 网上论坛徽标 trus...@googlegroups.com 帐号申请更改其 Google 网上论坛邀请设置。要确认此申请并更改选项，请使用下方的邀请设置

7/18/18

danteb...@gmail.com, … Bo Li4

7/18/18

est_library_size

Hi Asaf, You are right -- we multiply it by 1000, according to how CPK is defined. So you will get

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est_library_size

Hi Asaf, You are right -- we multiply it by 1000, according to how CPK is defined. So you will get

7/18/18

asaf...@gmail.com, Bo Li2

7/18/18

TCGA TRUST data

Hi Asaf, Thank you for your interest in our work. We have such a dataset and are currently analyzing

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TCGA TRUST data

Hi Asaf, Thank you for your interest in our work. We have such a dataset and are currently analyzing

7/18/18

jbea...@gmail.com, Bo Li2

7/16/18

CDR3 sequences in Nature Genetics Publication

Hi Jennifer, That problem came across before and was solved by using another computer. Would you

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CDR3 sequences in Nature Genetics Publication

Hi Jennifer, That problem came across before and was solved by using another computer. Would you

7/16/18

Feizhen Wu

6/20/18

running error when using mm10

Hi Bo, When I run below commands: bowtie2 -p 20 -x mm10_Bowtie2Index/genome -1 R1.fq -2 R2.fq -S test

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running error when using mm10

Hi Bo, When I run below commands: bowtie2 -p 20 -x mm10_Bowtie2Index/genome -1 R1.fq -2 R2.fq -S test

6/20/18

ting...@gmail.com, Bo Li7

6/20/18

Differences between *-TCR-ALL.txt and *-TCR-ALL.fa files in trust 3.0.1

That's helpful. Thank you, Bo. 在 2018年6月21日星期四 UTC+8上午9:59:23，Bo Li写道： Hi Ting, The long list of

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Differences between *-TCR-ALL.txt and *-TCR-ALL.fa files in trust 3.0.1

That's helpful. Thank you, Bo. 在 2018年6月21日星期四 UTC+8上午9:59:23，Bo Li写道： Hi Ting, The long list of

6/20/18

bioinfo...@gringene.org, Bo Li2

5/21/18

Report error if BAM index is not present

Can you paste your commandline for running TRUST? On Sun, May 20, 2018 at 7:01 PM, <bioinformatics

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Report error if BAM index is not present

Can you paste your commandline for running TRUST? On Sun, May 20, 2018 at 7:01 PM, <bioinformatics

5/21/18

Bo Li, guoy...@gmail.com4

4/25/18

Re: trust dependence regex install erro

Finally, it because I install Trust on our High-performance-computer, there are too many versions of

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Re: trust dependence regex install erro

Finally, it because I install Trust on our High-performance-computer, there are too many versions of

4/25/18

xfl...@gmail.com, zhang...@gmail.com2

4/22/18

Support for mouse genome mm9 or mm10?

We have made TRUST version 3.0 support mm10, please let us know if you have problems running it. 在

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Support for mouse genome mm9 or mm10?

We have made TRUST version 3.0 support mm10, please let us know if you have problems running it. 在

4/22/18

jbea...@gmail.com, Bo Li6

4/20/18

Discrepancy between *coverage.txt and *ALL.txt files in 3.0

Hi Jen, I would suggest you to read our method description in the 2017 NG paper. For PE library,

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Discrepancy between *coverage.txt and *ALL.txt files in 3.0

Hi Jen, I would suggest you to read our method description in the 2017 NG paper. For PE library,

4/20/18