Alternative Splicing and Functional Prediction

Sorry for the late reply. EnsMart100 will match to any hg38 but not T2T. Best, Nathan On Sun, Feb 18,

Hi Luz, We have encountered this issue on different machines with different operating systems as wx

Great, That should be fine. For dozens of BAM files I recommend running certain steps in parallel on

Hi Mohammad, You can, if the data is pre-processed, such that it already has basic (row or normalized

Hi Bianka, Actually, we primarily support RNA-Seq based analyses for species supported in Ensembl. In

Hi Chris, The issue is likely the naming of the FASTQ files, with the software not recognizing the

Hi Deema, We haven't worked with new Affymetrix profiles since about 2013, so we don't have

Hi Siawpeng, There is a log file produced for each fastq file pair when processed saved to the output

Hi Brian, The attached set of files provides an example of creating files to pass results from a

Dear Altanalyze team, Working with the new version of Altanalyze Release version 2.1.4.2 - 8/1/20.

Dear altanalyze, I tried to correct for Batch Effects using the GUI alatanalyze, but there seems to

Hi Eleonora, Nice work capturing neutrophils with decent expression! Combat is a reasonable way to

Hi Talat, It looks like Ensembl may have update some of their tables, but by the looks of it, you may

Hi Jason, Sorry for the late reply. Can you clarify what your input file types are and for which

Hi Brian, Sorry for the late reply. Please note that there is a new version of the software (2.1.4.2)

Hi Brian, Can you try moving the Demo folder out of the AltAnalyze program folder and try again with

Hello. I'm reading your publihsed article about Human Cell Atlase -- The Human Cell Atlas bone

Dear AltAnalyze team, I am contacting you because everytime I try to run the analysis I got the

Dear Dr. Nathan Salomonis. I'm reading your paper about Human Cell Atlas - "The Human Cell

Hi Brian, My apologies for the confusion. The current Kallisto version does not support Kallisto bus

Hi Lawrence, AltAnalyze supports a number of array formats for Affymetrix, but support for new

Hi Ghalib, Would it be possible to try on a different machine? I am not sure the error here, which we

Hi Matthias, You are correct in that the current AltAnalyze uses clf and associated files as a

Hi Kübra, Would you mind including the full log file saved to the output directory and a screenshot

Hi Brian, Let's walk through these various values: Isocounts = estimated number of reads for each

Hi, Confused on what the numbers in the files of expression input and output actually mean. Also,

Hi Nathan, thank you for your fast answer ! However, I still get some trouble when I try this pre-

Hi Huizeng, I think we understand the problem... Just carrying over the previous build of the viewer

Hi Brian, Looks like you are almost there but there are a few things to clarify. First, from the

Hi, Nathan, I downloaded the latest version (AltAnalyze_v.2.1.2_OSX-64bit.dmg) from https://