User: Uday Rangaswamy
Uday Rangaswamy • 150
- Reputation:
- 150
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- Trusted
- Location:
- Indian Institute of Technology, Madras, India
- Last seen:
- 5 days, 6 hours ago
- Joined:
- 2 years, 10 months ago
- Email:
- m*******@gmail.com
Posts by Uday Rangaswamy
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... Thanks. The count file of both the tools matched when I sorted it wrt name instead of the default samtools sort before passing it on to htseq-count.
So basically, you reckon I go ahead with the genecount file generated by STAR for the downstream analysis or should I count again for the rest of my ...
written 11 days ago by
Uday Rangaswamy • 150
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... Hi all,
I have the genecount file generated while using STAR for alignment. The second column of the genecount file (read count of unstranded hits) is supposed to be the exact same as the one counted using HTSeq-count in union mode. However, I noticed it happens to match with the genecount file gen ...
written 12 days ago by
Uday Rangaswamy • 150
• updated
12 days ago by
h.mon ♦ 32k
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... Our cluster is using SLURM for scheduling. The following resource request worked for me :
sbatch --ntasks=1 --cpus-per-task=32 --mem=32000mb --partition=regular1 --time=05:00:00 genome_generate.sh
Content of genoem_generate.sh :
#!/bin/sh
STAR --runThreadN 32 --runMode genomeGene ...
written 16 days ago by
Uday Rangaswamy • 150
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... Oh alright. I was under the impression that the command would distribute its load onto the available resources of the cluster by itself. So basically, I need to write a job script containing explicit resource allocation apart from the one contained in the command itself while using such shared clust ...
written 17 days ago by
Uday Rangaswamy • 150
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... Will check with the admin and get back to you. Thanks for your time. ...
written 17 days ago by
Uday Rangaswamy • 150
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... No, it's a shared cluster. However, there are no other processes running in parallel (checked using top command). I tried it using 40GB as well, but unfortunately, it still gets killed at the same point. ...
written 17 days ago by
Uday Rangaswamy • 150
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... Hi Genomax,
I checked for both conditions. The process is still getting killed at the same step. ...
written 18 days ago by
Uday Rangaswamy • 150
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... Hi _r_am,
I have 5TB of disk space to myself in the scratch section. I do have the write permission of the output folder :
[urangasw@login1 data]$ ls -al
total 12
drwxr-xr-x 3 urangasw fsg 4096 Jan 8 11:17 .
drwxr-xr-x 3 urangasw fsg 4096 Jan 8 11:16 ..
drwxrwxrwx 2 urangasw ...
written 18 days ago by
Uday Rangaswamy • 150
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5 follow
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... Hi,
I am running the following command to generate genome index using STAR aligner :
Softwares/STAR/bin/Linux_x86_64/STAR --runThreadN 8 --runMode genomeGenerate --genomeDir /scratch/urangasw/data/hg38_index --genomeFastaFiles /home/urangasw/data/genome/human/Homo_sapiens.GRCh38.dna.primary_as ...
written 18 days ago by
Uday Rangaswamy • 150
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Comment:
C: Bedtools BEDMAP usage
... foreach ($v1 as $value) {
$outputh = system("/home/uday/anaconda3/bin/bedmap --chrom ". $value ." --mean ppCkrtYdyJ_3.bed pc.bed >> ppCkrtYdyJ_f10.txt");
}
v1 contains unique chromosomes. I'm getting an empty file as output.
...
written 18 months ago by
Uday Rangaswamy • 150
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17 months ago,
created a post with more than 5 votes.
For DESeq2 modelling and Wald's test
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For Assembly conversion of large BED files
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For Differential expression gene analysis
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For eQTL analysis considering P-values
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For Hg19 reference genome for bedtools getfasta
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For Feature extraction from DNA sequence
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