User: archisman

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archisman0
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Posts by archisman

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How to download/save sample table presented at GEO2R
... I'm looking for a solution to download or save the sample table similar to the GEO2R for a GEO dataset. Here is an example: [https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE14468][1] [1]: https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE14468 I can use GEOquery package in R to do that. gse & ...
geo R geo2r written 3 months ago by archisman0
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Comment: C: HTseq does not generate any counts file
... Can you please guide me through how to do that? ...
written 8 months ago by archisman0
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Comment: C: HTseq does not generate any counts file
... Thanks for the reply. I just install pysam today. But it still does not work. I think I have to as my administrator to find the development library for the python. ...
written 8 months ago by archisman0
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Which statistical test to show the overlap of some genes in two different data is significant.
... Suppose I have a gene list of 470 genes that are induced in my study. I found that in other studies people already showed about 1000 genes were involved in the same kind of pathways but with the different model systems. Now, when I did an overlap of those 1000 genes with my 470 genes I found out of ...
R rna-seq written 8 months ago by archisman0 • updated 8 months ago by russhh5.5k
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HTseq does not generate any counts file
... Here is my code for generating counts from the BAM file. bsub -J "htseq-count" htseq-count \ -e /scratch/workspace/rnaseq/counts/err.txt \ -o /scratch/workspace/rnaseq/counts/log.out \ -f bam \ -r name \ -s no \ -a 10 \ -t exon \ -i gene_id \ -m intersection- ...
htseq-count rna-seq written 8 months ago by archisman0 • updated 8 months ago by Ido Tamir5.1k
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Comment: C: STAR alignment killed in between process
... Thanks, genomax for replaying. The process is failing after some time not immediately. Actually I was asking in the previous post that how to use SLURM ? Because `sbatch` command is not working and also I recently started working on node or Linux code in that matter. ...
written 9 months ago by archisman0
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STAR alignment process killed after sometime
... Hi, I am trying to run STAR alignment using the command below: STAR \ --runThreadN 8 \ --runMode genomeGenerate \ --genomeDir /scratch/workspace/rnaseq/STAR_genome/ \ --genomeFastaFiles /scratch/workspace/rnaseq/refs/GRCh38.d1.vd1.fa \ --sjdbOverhang 100 \ --sjdbGTFfi ...
alignment rna-seq written 9 months ago by archisman0
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Comment: C: STAR alignment killed
... MemTotal: 131484208 kB MemFree: 5941884 kB MemAvailable: 124402808 kB Buffers: 1712 kB Cached: 117349124 kB SwapCached: 609500 kB Active: 18888120 kB Inactive: 102006036 kB Active(anon): 2442888 kB Inac ...
written 9 months ago by archisman0 • updated 9 months ago by genomax89k
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Comment: A: STAR alignment killed
... I'm having the same problem as yours. Can you elaborate Slurm job? ...
written 9 months ago by archisman0

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