User: Uday Rangaswamy

gravatar for Uday Rangaswamy
Reputation:
150
Status:
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

<prev • 169 results • page 1 of 17 • next >
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Comment: C: STAR --quantMode GeneCounts vs HTSeq-count
... 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 Rangaswamy150
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STAR --quantMode GeneCounts vs HTSeq-count
... 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 ...
htseq next-gen star rna-seq sequencing written 12 days ago by Uday Rangaswamy150 • updated 12 days ago by h.mon32k
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Comment: C: STAR aligner index generating issues
... 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 Rangaswamy150
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Comment: C: STAR aligner index generating issues
... 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 Rangaswamy150
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Comment: C: STAR aligner index generating issues
... Will check with the admin and get back to you. Thanks for your time. ...
written 17 days ago by Uday Rangaswamy150
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Comment: C: STAR aligner index generating issues
... 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 Rangaswamy150
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Comment: C: STAR aligner index generating issues
... Hi Genomax, I checked for both conditions. The process is still getting killed at the same step. ...
written 18 days ago by Uday Rangaswamy150
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Comment: C: STAR aligner index generating issues
... 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 Rangaswamy150
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STAR aligner index generating issues
... 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 ...
genome alignment star rna-seq written 18 days ago by Uday Rangaswamy150
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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 Rangaswamy150

Latest awards to Uday Rangaswamy

Appreciated 17 months ago, created a post with more than 5 votes. For DESeq2 modelling and Wald's test
Popular Question 17 months ago, created a question with more than 1,000 views. For Differential expression gene analysis
Popular Question 17 months ago, created a question with more than 1,000 views. For Assembly conversion of large BED files
Popular Question 17 months ago, created a question with more than 1,000 views. For Differential expression gene analysis
Popular Question 17 months ago, created a question with more than 1,000 views. For eQTL analysis considering P-values
Popular Question 17 months ago, created a question with more than 1,000 views. For Using DESeq2 results for building a classifier
Popular Question 17 months ago, created a question with more than 1,000 views. For To obtain upstream DNA sequence by giving location
Popular Question 17 months ago, created a question with more than 1,000 views. For Note on DESeq2
Popular Question 17 months ago, created a question with more than 1,000 views. For BEDOPS bedmap tool usage
Popular Question 17 months ago, created a question with more than 1,000 views. For Hg19 reference genome for bedtools getfasta
Popular Question 17 months ago, created a question with more than 1,000 views. For Feature extraction from DNA sequence
Student 17 months ago, asked a question with at least 3 up-votes. For DESeq2 modelling and Wald's test
Popular Question 20 months ago, created a question with more than 1,000 views. For Differential expression gene analysis
Popular Question 21 months ago, created a question with more than 1,000 views. For DESeq2 modelling and Wald's test
Voter 23 months ago, voted more than 100 times.
Centurion 2.2 years ago, created 100 posts.
Supporter 2.8 years ago, voted at least 25 times.

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