User: arunprasanna83

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Posts by arunprasanna83

<prev • 54 results • page 1 of 6 • next >
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Comment: C: Intramodular connectivity and gene significance in WGCNA
... Hi, I am following the tutorial for WGCNA package, III. Using simulated data... Section 7. Module membership, Intramodular connectivity. Basically, above code is from section 7b. [Tutorial][1]. Essentially, this give gene significance against intramodular connectivity and helps to infer which of the ...
written 21 days ago by arunprasanna8340
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Intramodular connectivity and gene significance in WGCNA
... Hello, I performed WGCNA for 30 RNASeq samples ( a time-series data). I filtered genes that are significantly expressed over time-series (~3000 genes). I picked soft thresold power, constructed modules with signed network, intramodular connectivity and identified top hub genes in each module `cho ...
wgcna rna-seq co-expression network written 23 days ago by arunprasanna8340 • updated 21 days ago by Kevin Blighe56k
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sleuth fails with unusual error
... Hi, I ran the RNA-seq pipeline as follows in my workstation with 128GB RAM and several TBs storage: RNA-seq -i FASTQ/ -o DEG -j 10 --DAG --local -m 'alignment-free,deepTools_qc' --aligner 'HISAT2' --sampleSheet samplesheet1.tsv Cv2 The pipeline keeps failing at sleuth with the following error ...
#snakepipes written 6 weeks ago by arunprasanna8340
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Comment: C: Kallisto in snakePipes instead of salmon
... Hi @Devon Ryan please take a look at my edit. I have added the snippets of original gtf as well as annotation folder contents for your reference. Another observation is that, DE analysis fails not only if sample names have numbers but also special characters. For instance one of my samples had a nam ...
written 6 weeks ago by arunprasanna8340
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Kallisto in snakePipes instead of salmon
... Hi, Salmon version installed inside snakepipes env seems to be 0.7.x, whereas latest version -s 1.1.0. Following are the errors encountered: After it starts computing gene-level abundance: too many lines with [jointLog] [warning] Feature has no GFF ID [jointLog] [info] There were 0 tran ...
#snakepipes written 7 weeks ago by arunprasanna8340
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Comment: C: RNA-Seq pipeline fails during STAR alignment
... Yes !!. That worked. I un-installed it entirely and re-installed snakePipes. Now it is working fine ! ...
written 7 weeks ago by arunprasanna8340
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Comment: C: RNA-Seq pipeline fails during STAR alignment
... `snakePipes config` only gave a blank cursor and did not show any option like snakePipes info. Then I just edited the global defaults.yaml file !. Now I don't get the `mktemp` error. However, I get Error in STAR: EXITING because of FATAL ERROR: Genome version is INCOMPATIBLE with current STAR ...
written 7 weeks ago by arunprasanna8340
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RNA-Seq pipeline fails during STAR alignment
... Hi, I tried to run RNA-Seq pipeline in the following way: RNA-seq -i /data/TRANSCRIPTOME/CC7_TS/CC7_Clean -o ./TEST_OUT/ -j 10 --local --DAG -m 'alignment-free,deepTools_qc' --sampleSheet samplesheet.txt CC7v2 The dry-run went well without potential errors. When I submit the job, I get the fo ...
#snakepipes written 7 weeks ago by arunprasanna8340 • updated 7 weeks ago by Devon Ryan94k
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Comment: C: /bin/bash/ command not found
... The defaults.yaml file instructs to run snakemake directly after editing it ! ...
written 7 weeks ago by arunprasanna8340
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Comment: C: /bin/bash/ command not found
... I got /bin/bash only. ...
written 7 weeks ago by arunprasanna8340

Latest awards to arunprasanna83

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Motif prediction with MEME
Popular Question 3 months ago, created a question with more than 1,000 views. For Motif prediction with MEME
Popular Question 10 months ago, created a question with more than 1,000 views. For Troubleshooting interproscan standalone run
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Scholar 11 months ago, created an answer that has been accepted. For A: annotate gene feature
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