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SAMSA bioinformatics group

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Welcome to the SAMSA bioinformatics Google Group! Post here with any questions or issues with the SAMSA pipeline (http://www.github.com/transcript/SAMSA), and I'll do my best to provide answers.

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Debanjan Das, Sam Westreich2

8/29/25

Error in step 3

Hello, Do you have python installed on the computer where you are running this? Best, Sam On Fri, Aug

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Error in step 3

Hello, Do you have python installed on the computer where you are running this? Best, Sam On Fri, Aug

8/29/25

bob nichols, … Incredible Budget5

1/8/25

Loosing 30-35% of reads after DIAMOND annotation

SHOP BELOW weldingsupplyshop.com . Buy discounted welders, plasma cutters and welding safety gear by

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Loosing 30-35% of reads after DIAMOND annotation

SHOP BELOW weldingsupplyshop.com . Buy discounted welders, plasma cutters and welding safety gear by

1/8/25

Cheng Long, … Incredible Budget6

1/8/25

Error: Failed to create thread.

SHOP BELOW weldingsupplyshop.com . Buy discounted welders, plasma cutters and welding safety gear by

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Error: Failed to create thread.

SHOP BELOW weldingsupplyshop.com . Buy discounted welders, plasma cutters and welding safety gear by

1/8/25

Bella Borrero, Sam Westreich2

11/22/24

Error in step 1

Hi Bella, From the look of this, it's failing at step 1, where it runs Trimmomatic on the input

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Error in step 1

Hi Bella, From the look of this, it's failing at step 1, where it runs Trimmomatic on the input

11/22/24

Menia Gavriilidou

1/25/24

Parsing function names with more than one "[]"

Hi Sam, I have been using samsa2 for analyzing my data and I find it very nice and easy to use.

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Parsing function names with more than one "[]"

Hi Sam, I have been using samsa2 for analyzing my data and I find it very nice and easy to use.

1/25/24

Shandry Mmasetshaba

10/24/23

Function of each significant bacteria

Hi Samsa group, I would like to know if is possible to generate a table that shows signigicant

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Function of each significant bacteria

Hi Samsa group, I would like to know if is possible to generate a table that shows signigicant

10/24/23

megha...@gmail.com, Sam Westreich2

9/22/23

Is it possible to assess which taxonomy class/genus is contributing to the genes/pathways?

Hi Megha, Yes, there are some approaches for this. When you annotate the functions as sucrose

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Is it possible to assess which taxonomy class/genus is contributing to the genes/pathways?

Hi Megha, Yes, there are some approaches for this. When you annotate the functions as sucrose

9/22/23

Irishtsany Indira, Sam Westreich3

4/11/23

Rowvar usage instead of rowmean in heatmap making

Hi Irishtsany, You should be able to use pairwise comparisons to figure out the effects of some

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Rowvar usage instead of rowmean in heatmap making

Hi Irishtsany, You should be able to use pairwise comparisons to figure out the effects of some

4/11/23

Irishtsany Indira

4/7/23

Compatible statistical analysis for SAMSA2

Dear Sam, I want to ask about statistical analysis that is compatible with SAMSA2 pipeline. I've

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Compatible statistical analysis for SAMSA2

Dear Sam, I want to ask about statistical analysis that is compatible with SAMSA2 pipeline. I've

4/7/23

3/7/23

Getting a normalized table after aggregation

After aggregating my files, I have conducted an analysis using DESeq2. However, I am facing

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Getting a normalized table after aggregation

After aggregating my files, I have conducted an analysis using DESeq2. However, I am facing

3/7/23

1/6/23

Is there a known database for pathogenic microbial organisms (Bacteria and Viruses)?

Hi everyone, I am very new in the microbiome research field. I've got my results from Samsa2 and

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Is there a known database for pathogenic microbial organisms (Bacteria and Viruses)?

Hi everyone, I am very new in the microbiome research field. I've got my results from Samsa2 and

1/6/23

12/22/22

Any updates on Fungi database compatible with Samsa2

Hi Sam, I've noticed several people trying to include Fungi data in their analyses and almost all

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Any updates on Fungi database compatible with Samsa2

Hi Sam, I've noticed several people trying to include Fungi data in their analyses and almost all

12/22/22

12/18/22

error with standardized_DIAMOND_analysis_counter.py

Hello, I am having issues with standardized_DIAMOND_analysis_counter.py script I am getting an

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error with standardized_DIAMOND_analysis_counter.py

Hello, I am having issues with standardized_DIAMOND_analysis_counter.py script I am getting an

12/18/22

Aanuoluwa Adekoya2

12/2/22

Error in names(x) <- value in R studio

Hi Sam, I fixed all of my problems. Thanks! On Thursday, December 1, 2022 at 4:37:51 PM UTC-6

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Error in names(x) <- value in R studio

Hi Sam, I fixed all of my problems. Thanks! On Thursday, December 1, 2022 at 4:37:51 PM UTC-6

12/2/22

Aanuoluwa Adekoya, Sam Westreich9

11/16/22

Initial R analysis

Hi Sam, Thank you again for your help. When I removed the raw counts file, I got the functional

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Initial R analysis

Hi Sam, Thank you again for your help. When I removed the raw counts file, I got the functional

11/16/22

Dasiel Obregon2

11/16/22

Sortmerna database for funngi

Any update? On Tuesday, November 15, 2022 at 11:47:21 am UTC-5 Dasiel Obregon wrote: Dear all, It is

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Sortmerna database for funngi

Any update? On Tuesday, November 15, 2022 at 11:47:21 am UTC-5 Dasiel Obregon wrote: Dear all, It is

11/16/22

Indah Oktaviani, Sam Westreich2

11/12/22

Error in DIAMOND_specific_organism_retriever.py

Hi Indah, This looks pretty straightforward; can you confirm that the infile, 'view_RMTA1a.m8

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Error in DIAMOND_specific_organism_retriever.py

Hi Indah, This looks pretty straightforward; can you confirm that the infile, 'view_RMTA1a.m8

11/12/22

Moya Farahyah, … Amanda Zahorik3

11/3/22

Annoting to a more general taxonomic classification & functional annotation using other database

Hi Sam, Jumping in because I was looking for this solution and wanted to follow up. I ran the script

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Annoting to a more general taxonomic classification & functional annotation using other database

Hi Sam, Jumping in because I was looking for this solution and wanted to follow up. I ran the script

11/3/22

Jordyn Broadbent, Sam Westreich2

6/14/22

Step 1/Trimmomatic issues with matching up paired-read files

Hey Jordyn, Could you share the names of the files in your input folder? You could run "ls"

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Step 1/Trimmomatic issues with matching up paired-read files

Hey Jordyn, Could you share the names of the files in your input folder? You could run "ls"

6/14/22

radz150193, … Kabir Peay6

6/10/22

Is the SEED database suitable for fungi?

It's been two years since this post and I was wondering if there are any updated recommendations

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Is the SEED database suitable for fungi?

It's been two years since this post and I was wondering if there are any updated recommendations

6/10/22

6/10/22

Error with Diamond

Never mind - figured out that this was just a problem related to the log-in node environment I was

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Error with Diamond

Never mind - figured out that this was just a problem related to the log-in node environment I was

6/10/22

Teresa Mccarrell, Sam Westreich3

6/8/22

Error with DIAMOND_analysis_counter.py?

I had downloaded this database as a file called "nr.gz," which became "nr" with

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Error with DIAMOND_analysis_counter.py?

I had downloaded this database as a file called "nr.gz," which became "nr" with

6/8/22

Vinícius Rodovalho

5/23/22

Is it possible to obtain RefSeq IDs instead of more general annotation?

Hello everybody, I have a doubt concerning the aggregation step of the pipeline, the one that

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Is it possible to obtain RefSeq IDs instead of more general annotation?

Hello everybody, I have a doubt concerning the aggregation step of the pipeline, the one that

5/23/22

Michael R, … Daniel Revillini4

4/29/22

Concerns with alignment accuracy

Hello all, Interested to find out if you've ever resolved the analyses here? I am running into

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Concerns with alignment accuracy

Hello all, Interested to find out if you've ever resolved the analyses here? I am running into

4/29/22

Daniel Revillini

3/26/22

PEAR timeout issue through HPC

HI Sam, First, thanks for SAMSA2, this is super helpful to someone who has almost entirely done

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PEAR timeout issue through HPC

HI Sam, First, thanks for SAMSA2, this is super helpful to someone who has almost entirely done

3/26/22

2/25/22

Error with R scritps (DEseq_stats.R)

Hello, I had rthis error when I try to run DESeq_stats. /run_DESeq_stats.R: line 4: syntax error near

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Error with R scritps (DEseq_stats.R)

Hello, I had rthis error when I try to run DESeq_stats. /run_DESeq_stats.R: line 4: syntax error near

2/25/22

fio...@appstate.edu, Sam Westreich9

12/6/21

index out of range with standardized_DIAMOND_analysis_counter.py

Hi Cara, For question 1, can you share what the error that the Python script is reporting? If you

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index out of range with standardized_DIAMOND_analysis_counter.py

Hi Cara, For question 1, can you share what the error that the Python script is reporting? If you

12/6/21

11/11/21

Blank Pie charts

Hi Sam, For some reason I keep getting blank pie charts with no errors in code, and I traced it back

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Blank Pie charts

Hi Sam, For some reason I keep getting blank pie charts with no errors in code, and I traced it back

11/11/21

lusine Khachatryan, Sam Westreich3

10/25/21

Host sequences filtering

Dear Sam, Thank you! Yes, what you've described (mapping on human genome after the ribodepletion)

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Host sequences filtering

Dear Sam, Thank you! Yes, what you've described (mapping on human genome after the ribodepletion)

10/25/21

Eric Gathirwa, … Sam Westreich4

8/9/21

Running DESeq2 stats with one control

Hey Elisa, I'm not sure if folks have tried this before, but there are some tools for assembly

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Running DESeq2 stats with one control

Hey Elisa, I'm not sure if folks have tried this before, but there are some tools for assembly

8/9/21

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