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Hi Brian,Can you send your log file from AltAnalyze and a screenshot of these directories? The default ICGS option for Minimum number of samples differing to 2 or 3 and correlation to 0.6 for this study design.Best,Nathan
On Thu, Jul 2, 2020 at 12:36 AM Brian Estevez <beste...@gmail.com> wrote:
--Hi,I am using the latest version for PC 2.1.4.1My goal is to do ICGS on single cell rna sequencing fastq files. From GUI, I first run raw sequence or processed on 6 fastq files: from 2 samples, each with index, cdna and cell barcode files). I do this in order to get a Kalisto expression input file and re-run for ICGS using process expression file mode.Oddly, there are two expression input folders being generated upon completion of first run on my fastq files:1) in the specified output folder and another one 2) alongside the fastq files.There are 3 files in '1)' two folders that correspond to two of my samples containing files such as abundance.h5, abundance.tsv, and run_info.json, and a log.txt file.There are no files in ' 2)' ExpressionInput/KallistoSo I use the exp.txt file in Kalisto_Results folder. I run analysis and get the error: indexerror list inder out of range.What should I try next?-Brian
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Hi Brian,Can you send your log file from AltAnalyze and a screenshot of these directories? The default ICGS option for Minimum number of samples differing to 2 or 3 and correlation to 0.6 for this study design.Best,Nathan
On Thu, Jul 2, 2020 at 12:36 AM Brian Estevez <beste...@gmail.com> wrote:
--Hi,I am using the latest version for PC 2.1.4.1My goal is to do ICGS on single cell rna sequencing fastq files. From GUI, I first run raw sequence or processed on 6 fastq files: from 2 samples, each with index, cdna and cell barcode files). I do this in order to get a Kalisto expression input file and re-run for ICGS using process expression file mode.Oddly, there are two expression input folders being generated upon completion of first run on my fastq files:1) in the specified output folder and another one 2) alongside the fastq files.There are 3 files in '1)' two folders that correspond to two of my samples containing files such as abundance.h5, abundance.tsv, and run_info.json, and a log.txt file.There are no files in ' 2)' ExpressionInput/KallistoSo I use the exp.txt file in Kalisto_Results folder. I run analysis and get the error: indexerror list inder out of range.What should I try next?-Brian
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python AltAnalyze.py --platform RNASeq --species Hs --restrictBy protein_coding --excludeCellCycle no --removeOutliers yes --row_method hopach --ChromiumSparseMatrix /Users/GitHub/tests/demo_data/10X/input/cancer.h5 --output Users/GitHub/tests/demo_data/10X/input --runICGS yes --expname cancer --downsample 2500
For a counts file
python AltAnalyze.py --platform RNASeq --species Hs --restrictBy protein_coding --excludeCellCycle no --removeOutliers yes --row_method hopach --ChromiumSparseMatrix /Users/GitHub/tests/demo_data/10X/input/cancer.h5 --output Users/GitHub/tests/demo_data/10X/input --runICGS yes --expname cancer --dataFormat counts
You could also run Kallisto bus to get the input files, which I believe is fairly straight forward. Kallisto-bus is on our timeline but was delayed.
Best,
Nathan
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