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Rodrigo de Alexandre, … Brian Haas5

Jan 28

CTAT-Splicing different calls in different genomes version

Hi there, thanks for the response. So for this case this AR alternative splicing is not in an

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CTAT-Splicing different calls in different genomes version

Hi there, thanks for the response. So for this case this AR alternative splicing is not in an

Jan 28

Elad Herz, Brian Haas2

11/28/25

Hi Elad, The dfam step can run for a long time, but assuming it does actually finish at some point,

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Hi Elad, The dfam step can run for a long time, but assuming it does actually finish at some point,

11/28/25

Francisco, Brian Haas2

11/28/25

FUSION_CDS and FUSION_TRANSL sequences

Hi Fran, This part is just taking into account the fusion breakpoints and the reference annotations.

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FUSION_CDS and FUSION_TRANSL sequences

Hi Fran, This part is just taking into account the fusion breakpoints and the reference annotations.

11/28/25

Martin, Brian Haas2

9/12/25

Question regarding reported PFAM domains and coordinates in STAR-Fusion --fusioninspector validate results

Hi Martin, The Pham hits are precomputed based on the reference annotations and the coordinates

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Question regarding reported PFAM domains and coordinates in STAR-Fusion --fusioninspector validate results

Hi Martin, The Pham hits are precomputed based on the reference annotations and the coordinates

9/12/25

evan, Brian Haas8

6/19/25

detect gene fusion between virus and human

Nice detective work there! One thought would be to pad your viral genome by a few kb of N characters

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detect gene fusion between virus and human

Nice detective work there! One thought would be to pad your viral genome by a few kb of N characters

6/19/25

filippo martignano, Brian Haas2

6/9/25

clarification about FusionInspector manuscript

Hi Filippo, The full list of TARGET samples we examined are listed here: https://github.com/

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clarification about FusionInspector manuscript

Hi Filippo, The full list of TARGET samples we examined are listed here: https://github.com/

6/9/25

Beatrice Awasthi

4/21/25

infercnv workflow won't start

Hello, I am new to running infercnv and trying to run it on a dataset of 100000 cells and 40000 genes

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infercnv workflow won't start

Hello, I am new to running infercnv and trying to run it on a dataset of 100000 cells and 40000 genes

4/21/25

Luobin Yang, Brian Haas3

4/16/25

Do we need to run "ctat-LR-fusion --prep_reference" once for each sample?

Hi Brian, thanks for the clarification! On Wednesday, April 16, 2025 at 5:50:57 AM UTC-6 bh...@

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Do we need to run "ctat-LR-fusion --prep_reference" once for each sample?

Hi Brian, thanks for the clarification! On Wednesday, April 16, 2025 at 5:50:57 AM UTC-6 bh...@

4/16/25

Bole Pan, Brian Haas2

4/14/25

CTAT_HumanFusionLib construction to detect target gene fusion

Hi, If GeneX is something that's not a normal part of the human genome, then you'd need to

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CTAT_HumanFusionLib construction to detect target gene fusion

Hi, If GeneX is something that's not a normal part of the human genome, then you'd need to

4/14/25

Sharon Bader, Brian Haas2

4/8/25

Troubleshooting Fusion Detection in Pooled RNA-seq Data

Hi Sharon, If the fusions are going to be rare events, then you'll want to run STAR-Fusion with

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Troubleshooting Fusion Detection in Pooled RNA-seq Data

Hi Sharon, If the fusions are going to be rare events, then you'll want to run STAR-Fusion with

4/8/25

3/5/25

Additional Steps for Customised Gencode version for CTAT-Mutations

Hi all, I am trying to use CTAT-Mutations on some human RNA-Seq samples. Due to the need for using it

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Additional Steps for Customised Gencode version for CTAT-Mutations

Hi all, I am trying to use CTAT-Mutations on some human RNA-Seq samples. Due to the need for using it

3/5/25

2/10/25

Announcement: CTAT-LR-Fusion release v1.1.0

Greetings all! A new version of CTAT-LR-Fusion is now available: https://github.com/TrinityCTAT/CTAT-

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Announcement: CTAT-LR-Fusion release v1.1.0

Greetings all! A new version of CTAT-LR-Fusion is now available: https://github.com/TrinityCTAT/CTAT-

2/10/25

Asher Preska Steinberg, Brian Haas5

2/9/25

predicted CDS regions in CTAT-LR-Fusion

Okay great, thanks for your help! Best, Asher On Sunday, February 9, 2025 at 7:48:59 AM UTC-5 bh...@

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predicted CDS regions in CTAT-LR-Fusion

Okay great, thanks for your help! Best, Asher On Sunday, February 9, 2025 at 7:48:59 AM UTC-5 bh...@

2/9/25

Aaron De Cock, Brian Haas2

1/22/25

CTAT_splicing no cancer introns identified

Hi Aaron, It should just require that the cancer_splicing_lib/cancer_splicing.idx be incorporated

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CTAT_splicing no cancer introns identified

Hi Aaron, It should just require that the cancer_splicing_lib/cancer_splicing.idx be incorporated

1/22/25

Robert Forsyth, … Asher Preska Steinberg8

12/20/24

CTAT_LR Fusion Visualization

Hi Brian, Thanks for your help. Sounds good, let me follow-up with you on github now. Best, Asher On

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CTAT_LR Fusion Visualization

Hi Brian, Thanks for your help. Sounds good, let me follow-up with you on github now. Best, Asher On

12/20/24

Asher Preska Steinberg, Brian Haas4

12/18/24

using FusionInspector with long-read data?

Using more CPUs should definitely speed up certain parts, particularly those involving minimap2 (two

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using FusionInspector with long-read data?

Using more CPUs should definitely speed up certain parts, particularly those involving minimap2 (two

12/18/24

小林賢子, Brian Haas4

11/25/24

Trying download T2T-CHM13

The system uses checkpoint so it can pick up where earlier jobs left off. If you want to rerun with

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Trying download T2T-CHM13

The system uses checkpoint so it can pick up where earlier jobs left off. If you want to rerun with

11/25/24

11/13/24

Announcement: FusionInspector Release v2.10.0

Greetings all, A new release for FusionInspector is now available: https://github.com/FusionInspector

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Announcement: FusionInspector Release v2.10.0

Greetings all, A new release for FusionInspector is now available: https://github.com/FusionInspector

11/13/24

Sean Evans, Brian Haas2

11/7/24

Yeast CTAT genome

Hi, You can build your own ctat genome lib via: https://github.com/TrinityCTAT/ctat-genome-lib-

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Yeast CTAT genome

Hi, You can build your own ctat genome lib via: https://github.com/TrinityCTAT/ctat-genome-lib-

11/7/24

10/14/24

Re: using ctat_mutation with single-end samples

Yes, if you use just --left then it should run with single-end data. On Mon, Oct 14, 2024 at 6:06 AM

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Re: using ctat_mutation with single-end samples

Yes, if you use just --left then it should run with single-end data. On Mon, Oct 14, 2024 at 6:06 AM

10/14/24

10/8/24

Announcement: CTAT-LR-Fusion Release v1.0.0

Greetings all, A new release for CTAT-LR-Fusion (fusion detection using long isoform read sequences)

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Announcement: CTAT-LR-Fusion Release v1.0.0

Greetings all, A new release for CTAT-LR-Fusion (fusion detection using long isoform read sequences)

10/8/24

9/28/24

ctat-LR-fusion pacbio webinar now available on youtube

Greetings all, For those interested in our CTAT-LR-Fusion software for finding fusions based on long

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ctat-LR-fusion pacbio webinar now available on youtube

Greetings all, For those interested in our CTAT-LR-Fusion software for finding fusions based on long

9/28/24

7/30/24

Inquiry About inferCNV plot for two samples

Hi inferCNV team, I have a question regarding the usage of inferCNV. Have you run inferCNV on two

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Inquiry About inferCNV plot for two samples

Hi inferCNV team, I have a question regarding the usage of inferCNV. Have you run inferCNV on two

7/30/24

Dmitry Kazantsev

7/15/24

Can't extract data from infercnv object

Hello, I'm using inferCNV to compare tumors before and after therapy failure. I'd like to

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Can't extract data from infercnv object

Hello, I'm using inferCNV to compare tumors before and after therapy failure. I'd like to

7/15/24

6/29/24

Announcement: CTAT-Mutations v4.2.0 available

Please note, for long-read calling, the CTAT-Mutations v4.2.0 - while still performing well - was not

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Announcement: CTAT-Mutations v4.2.0 available

Please note, for long-read calling, the CTAT-Mutations v4.2.0 - while still performing well - was not

6/29/24

小林賢子, Brian Haas2

6/19/24

About COSMIC fusions

Hi, It doesn't look like there's a pass-through option for this in STAR-Fusion, and so you

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About COSMIC fusions

Hi, It doesn't look like there's a pass-through option for this in STAR-Fusion, and so you

6/19/24

5/29/24

Intrachromosomal neighbors overlap

Hi CTAT-LR-fusion team, I used CTAT-LR-fusion to detect fusion events in PacBio and Nanopore long-

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Intrachromosomal neighbors overlap

Hi CTAT-LR-fusion team, I used CTAT-LR-fusion to detect fusion events in PacBio and Nanopore long-

5/29/24

5/15/24

Re: CTAT-LR-Fusion make error

Hi, We have docker and singularity images available in case that's an option for you: https://

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Re: CTAT-LR-Fusion make error

Hi, We have docker and singularity images available in case that's an option for you: https://

5/15/24

Noura Tbeileh, Nadia Correia3

4/10/24

infercnv annotation file cell names vs raw matrix file cell names not matching

HI there I have the exactly same problem and don't know how to solve it. Maybe you can tell me

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infercnv annotation file cell names vs raw matrix file cell names not matching

HI there I have the exactly same problem and don't know how to solve it. Maybe you can tell me

4/10/24

3/14/24

Announcement: CTAT-Mutations Release v4.1.0

Greetings all, We have a new release for CTAT-Mutations (v4.1.0): https://github.com/NCIP/ctat-

unread,

Announcement: CTAT-Mutations Release v4.1.0

Greetings all, We have a new release for CTAT-Mutations (v4.1.0): https://github.com/NCIP/ctat-

3/14/24

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