User: archisman

gravatar for archisman
archisman0
Reputation:
0
Status:
New User
Last seen:
1 day, 7 hours ago
Joined:
11 months, 1 week ago
Email:
a*********@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by archisman

<prev • 9 results • page 1 of 1 • next >
0
votes
0
answers
252
views
0
answers
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 5 months ago by archisman0
0
votes
1
answer
217
views
1
answers
Comment: C: HTseq does not generate any counts file
... Can you please guide me through how to do that? ...
written 10 months ago by archisman0
0
votes
1
answer
217
views
1
answers
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 10 months ago by archisman0
1
vote
1
answer
224
views
1
answer
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 10 months ago by archisman0 • updated 10 months ago by russhh5.5k
0
votes
1
answer
217
views
1
answer
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 10 months ago by archisman0 • updated 10 months ago by Ido Tamir5.1k
0
votes
0
answers
478
views
0
answers
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 11 months ago by archisman0
1
vote
0
answers
478
views
0
answers
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 11 months ago by archisman0
0
votes
1
answer
4.5k
views
1
answers
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 11 months ago by archisman0 • updated 11 months ago by genomax92k
0
votes
1
answer
4.5k
views
1
answers
Comment: A: STAR alignment killed
... I'm having the same problem as yours. Can you elaborate Slurm job? ...
written 11 months ago by archisman0

Latest awards to archisman

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2208 users visited in the last hour