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Alternative Splicing and Functional Prediction
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Nathan Salomonis
5/7/24
Re: Error when trying to get pathway analysis
Greetings, Perhaps the destination folder has a write limitation, otherwise, it may be due to the
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Re: Error when trying to get pathway analysis
Greetings, Perhaps the destination folder has a write limitation, otherwise, it may be due to the
5/7/24
wu__kang
,
Nathan Salomonis
5
2/23/24
about database version
Sorry for the late reply. EnsMart100 will match to any hg38 but not T2T. Best, Nathan On Sun, Feb 18,
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about database version
Sorry for the late reply. EnsMart100 will match to any hg38 but not T2T. Best, Nathan On Sun, Feb 18,
2/23/24
Nathan Salomonis
9/20/22
Re: AltAnalyze User Group Trouble for running AltAnalyze
Hi Luz, We have encountered this issue on different machines with different operating systems as wx
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Re: AltAnalyze User Group Trouble for running AltAnalyze
Hi Luz, We have encountered this issue on different machines with different operating systems as wx
9/20/22
AltAnalyze CCHMC
, …
Nathan Salomonis
4
6/21/21
Re: from Molkentin Lab, CCHMC: regd. AtlAnalyze analysis pipeline.
Great, That should be fine. For dozens of BAM files I recommend running certain steps in parallel on
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Re: from Molkentin Lab, CCHMC: regd. AtlAnalyze analysis pipeline.
Great, That should be fine. For dozens of BAM files I recommend running certain steps in parallel on
6/21/21
Mohammad Alfrad Nobel Bhuiyan
,
Nathan Salomonis
2
6/21/21
Proteomics data
Hi Mohammad, You can, if the data is pre-processed, such that it already has basic (row or normalized
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Proteomics data
Hi Mohammad, You can, if the data is pre-processed, such that it already has basic (row or normalized
6/21/21
bian...@gmx.de
,
Nathan Salomonis
2
4/8/21
Please help
Hi Bianka, Actually, we primarily support RNA-Seq based analyses for species supported in Ensembl. In
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Please help
Hi Bianka, Actually, we primarily support RNA-Seq based analyses for species supported in Ensembl. In
4/8/21
María Carolina Gallego Iradi
, …
Nathan Salomonis
3
4/8/21
Kallisto failure No such file abundance.tsv
Hi Chris, The issue is likely the naming of the FASTQ files, with the software not recognizing the
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Kallisto failure No such file abundance.tsv
Hi Chris, The issue is likely the naming of the FASTQ files, with the software not recognizing the
4/8/21
AL WADAANI, DEEMAH
,
Nathan Salomonis
2
2/22/21
library files for Clariom D using ALT analysis
Hi Deema, We haven't worked with new Affymetrix profiles since about 2013, so we don't have
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library files for Clariom D using ALT analysis
Hi Deema, We haven't worked with new Affymetrix profiles since about 2013, so we don't have
2/22/21
Siawpeng Er
,
Nathan Salomonis
2
10/12/20
Kallisto output
Hi Siawpeng, There is a log file produced for each fastq file pair when processed saved to the output
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Kallisto output
Hi Siawpeng, There is a log file produced for each fastq file pair when processed saved to the output
10/12/20
beste...@gmail.com
, …
Schnell, Daniel (Dan)
4
10/12/20
Loading Seurat object into Cell Harmony
Hi Brian, The attached set of files provides an example of creating files to pass results from a
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Loading Seurat object into Cell Harmony
Hi Brian, The attached set of files provides an example of creating files to pass results from a
10/12/20
Brian Estevez
,
Nathan Salomonis
3
9/18/20
IOError: Error only with Cell Harmony
Dear Altanalyze team, Working with the new version of Altanalyze Release version 2.1.4.2 - 8/1/20.
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IOError: Error only with Cell Harmony
Dear Altanalyze team, Working with the new version of Altanalyze Release version 2.1.4.2 - 8/1/20.
9/18/20
Nadiah Abu
9/17/20
Error in COMBAT- Agilent Microarray
Dear altanalyze, I tried to correct for Batch Effects using the GUI alatanalyze, but there seems to
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Error in COMBAT- Agilent Microarray
Dear altanalyze, I tried to correct for Batch Effects using the GUI alatanalyze, but there seems to
9/17/20
LUSITO ELEONORA
,
Nathan Salomonis
2
8/25/20
cellHarmony: combat on scRNA-Seq
Hi Eleonora, Nice work capturing neutrophils with decent expression! Combat is a reasonable way to
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cellHarmony: combat on scRNA-Seq
Hi Eleonora, Nice work capturing neutrophils with decent expression! Combat is a reasonable way to
8/25/20
Talat Yasoob
,
Nathan Salomonis
2
8/20/20
I am having problem to download the species "Oryctolagus cuniculus" in AltAnalyze
Hi Talat, It looks like Ensembl may have update some of their tables, but by the looks of it, you may
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I am having problem to download the species "Oryctolagus cuniculus" in AltAnalyze
Hi Talat, It looks like Ensembl may have update some of their tables, but by the looks of it, you may
8/20/20
JASON BYRNE
,
Nathan Salomonis
2
8/3/20
Struggling to use AltAnalyze.
Hi Jason, Sorry for the late reply. Can you clarify what your input file types are and for which
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Struggling to use AltAnalyze.
Hi Jason, Sorry for the late reply. Can you clarify what your input file types are and for which
8/3/20
Brian Estevez
,
Nathan Salomonis
2
8/2/20
Comparison to bone marrow atlas and Cell harmony
Hi Brian, Sorry for the late reply. Please note that there is a new version of the software (2.1.4.2)
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Comparison to bone marrow atlas and Cell harmony
Hi Brian, Sorry for the late reply. Please note that there is a new version of the software (2.1.4.2)
8/2/20
Nathan Salomonis
,
beste...@gmail.com
3
7/26/20
Re: AltAnalyze User Group IOError: Error only with Cell Harmony
Hi Brian, Can you try moving the Demo folder out of the AltAnalyze program folder and try again with
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Re: AltAnalyze User Group IOError: Error only with Cell Harmony
Hi Brian, Can you try moving the Demo folder out of the AltAnalyze program folder and try again with
7/26/20
Nathan Salomonis
,
paran...@gmail.com
2
7/7/20
Re: KeyError: 'Hs' at the first command in running procedure of the supplementary document your published article
Hello. I'm reading your publihsed article about Human Cell Atlase -- The Human Cell Atlas bone
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Re: KeyError: 'Hs' at the first command in running procedure of the supplementary document your published article
Hello. I'm reading your publihsed article about Human Cell Atlase -- The Human Cell Atlas bone
7/7/20
Dr. Christian Smolka
7/7/20
fatal error problem
Dear AltAnalyze team, I am contacting you because everytime I try to run the analysis I got the
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fatal error problem
Dear AltAnalyze team, I am contacting you because everytime I try to run the analysis I got the
7/7/20
Joung-hwan Oh
7/7/20
Can I get any advice about the error rising when I tried to use AltAnalyze?
Dear Dr. Nathan Salomonis. I'm reading your paper about Human Cell Atlas - "The Human Cell
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Can I get any advice about the error rising when I tried to use AltAnalyze?
Dear Dr. Nathan Salomonis. I'm reading your paper about Human Cell Atlas - "The Human Cell
7/7/20
Brian Estevez
,
Nathan Salomonis
5
7/2/20
expinput kallisto folder empty
Hi Brian, My apologies for the confusion. The current Kallisto version does not support Kallisto bus
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expinput kallisto folder empty
Hi Brian, My apologies for the confusion. The current Kallisto version does not support Kallisto bus
7/2/20
Lawrence McKinney
,
Nathan Salomonis
2
10/28/19
APT error in Alt Analyze
Hi Lawrence, AltAnalyze supports a number of array formats for Affymetrix, but support for new
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APT error in Alt Analyze
Hi Lawrence, AltAnalyze supports a number of array formats for Affymetrix, but support for new
10/28/19
Ghalib Bardai
,
Nathan Salomonis
4
9/3/19
Kallisto failed due to an unknown error
Hi Ghalib, Would it be possible to try on a different machine? I am not sure the error here, which we
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Kallisto failed due to an unknown error
Hi Ghalib, Would it be possible to try on a different machine? I am not sure the error here, which we
9/3/19
Matthias Kirsch
,
Nathan Salomonis
2
8/22/19
trouble running altanalyze
Hi Matthias, You are correct in that the current AltAnalyze uses clf and associated files as a
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trouble running altanalyze
Hi Matthias, You are correct in that the current AltAnalyze uses clf and associated files as a
8/22/19
Kübra Çelikbaş
,
Nathan Salomonis
2
4/20/19
Altanalyze software error
Hi Kübra, Would you mind including the full log file saved to the output directory and a screenshot
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Altanalyze software error
Hi Kübra, Would you mind including the full log file saved to the output directory and a screenshot
4/20/19
Brian Estevez
,
Nathan Salomonis
2
4/20/19
Understanding tables in Altanlyze Results and Gene expression in control samples
Hi Brian, Let's walk through these various values: Isocounts = estimated number of reads for each
unread,
Understanding tables in Altanlyze Results and Gene expression in control samples
Hi Brian, Let's walk through these various values: Isocounts = estimated number of reads for each
4/20/19
beste...@gmail.com
4/20/19
What do the numbers in files Exp., Counts., and DATASET. mean?
Hi, Confused on what the numbers in the files of expression input and output actually mean. Also,
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What do the numbers in files Exp., Counts., and DATASET. mean?
Hi, Confused on what the numbers in the files of expression input and output actually mean. Also,
4/20/19
david....@gmail.com
,
Nathan Salomonis
3
3/22/19
Trouble for running AltAnalyze
Hi Nathan, thank you for your fast answer ! However, I still get some trouble when I try this pre-
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Trouble for running AltAnalyze
Hi Nathan, thank you for your fast answer ! However, I still get some trouble when I try this pre-
3/22/19
vbadillol...@gmail.com
, …
Nathan Salomonis
6
3/8/19
Error AltAnalyze Viewer
Hi Huizeng, I think we understand the problem... Just carrying over the previous build of the viewer
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Error AltAnalyze Viewer
Hi Huizeng, I think we understand the problem... Just carrying over the previous build of the viewer
3/8/19
beste...@gmail.com
,
Nathan Salomonis
2
3/3/19
Help Assigning groups and comparisons for RNASEQ files
Hi Brian, Looks like you are almost there but there are a few things to clarify. First, from the
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Help Assigning groups and comparisons for RNASEQ files
Hi Brian, Looks like you are almost there but there are a few things to clarify. First, from the
3/3/19