User: tarek.mohamed

Reputation:
0
Status:
New User
Location:
Last seen:
4 weeks ago
Joined:
1 year, 10 months ago
Email:
t************@northwestern.edu

Posts by tarek.mohamed

<prev • 30 results • page 1 of 3 • next >
0
votes
0
answers
229
views
0
answers
subread aligner for DNA WGS_how to increase the speed of subread?
... Hi All, I am trying to align one DNA whole genome sequence file using subread, the sequence reads are paired end, 150 bp reads. I used 'thread=64' and 216 core (9 nodes, 24 core each). but after two days it processed only 15% and I had to kill the job. I am using the university quest, so basically ...
subread speed written 14 months ago by tarek.mohamed0
0
votes
3
answers
398
views
3
answers
Comment: C: rsubread versus BWA ( Burrows-Wheeler Alignmener) for whole genome alignment
... Hi wie, One more questions. I tried subread to align whole genome sequence from one sample (paired end, 150 bp reads) and I used 'thread=64' and 216 core (9 nodes, 24 core each). but after two days it processed only 15% and I had to kill the job. I am using the university quest, so basically I ca ...
written 14 months ago by tarek.mohamed0
0
votes
3
answers
398
views
3
answers
Comment: C: rsubread versus BWA ( Burrows-Wheeler Alignmener) for whole genome alignment
... Hi Wei, I have already specified isBAM =FALSE. I have added here the sessionInfo()  >exactSNP(SNPAnnotationFile="All_20151104.vcf",readFile="CH1_0uM_subjunc.sam",isBAM=FALSE,refGenomeFile="BSgenome.Hsapiens.NCBI.GRCh38.fasta",outputFile="subread_jg4.sam.vcf",nthreads=40)   > sessionInfo() ...
written 14 months ago by tarek.mohamed0
0
votes
3
answers
398
views
3
answers
Comment: C: rsubread versus BWA ( Burrows-Wheeler Alignmener) for whole genome alignment
...  >library(Rsubread) > setwd("/projects/b1042/BurridgeLab/rnaseq_rarg") >exactSNP(SNPAnnotationFile="All_20151104.vcf",readFile="subread_jg4.sam",isBAM=FALSE,refGenomeFile="BSgenome.Hsapiens.NCBI.GRCh38.fasta",outputFile="subread_jg4.sam.vcf",nthreads=40)              //==================== ...
written 14 months ago by tarek.mohamed0
0
votes
3
answers
398
views
3
answers
Comment: C: rsubread versus BWA ( Burrows-Wheeler Alignmener) for whole genome alignment
... Hi Wei, I tried this with the unzipped file and it returns  *** caught segfault *** address 0x7fff9a688000, cause 'memory not mapped' Thanks Tarek ...
written 14 months ago by tarek.mohamed0
0
votes
3
answers
398
views
3
answers
Comment: C: rsubread versus BWA ( Burrows-Wheeler Alignmener) for whole genome alignment
... Hi Wei, Thanks for your reply. I am processing whole genome sequencing data, following to alignment, I want to call SNPs within different samples (100 samples). SNP data will be used to perform a downstream GWAS. DO you think I can use exactSNP() to call SNPs or shall I stick to GATK.   Thanks ...
written 14 months ago by tarek.mohamed0
1
vote
3
answers
398
views
3
answers
rsubread versus BWA ( Burrows-Wheeler Alignmener) for whole genome alignment
... Hi All, I have some whole genome sequencing data that were generated from illumina hiseq platform. as a first step, I will align the fastq file to a reference genome. Can I use Rsubread for that?  I have used it for RNAseq mapping before and it was very good, I got 90% of the read were mapped to t ...
rsubread ngs bwa written 14 months ago by tarek.mohamed0 • updated 14 months ago by Wei Shi2.7k
0
votes
1
answer
294
views
1
answer
rsubread exactsnp ERROR "memory not mapped"
... Hi All, I am trying to call SNPs from RNAseq data. I am using exactSNP function from Rsubread package.  I got an error ( *** caught segfault *** address (nil), cause 'memory not mapped') The script is as follows; >library(Rsubread) >exactSNP(SNPAnnotationFile="All_20151104.vcf.gz",readFile ...
rsubread exactsnp written 14 months ago by tarek.mohamed0 • updated 14 months ago by Wei Shi2.7k
0
votes
1
answer
628
views
1
answer
installation of package 'rmarkdown' had non-zero exit status
...   I had problems installing rmarkdown updated version in Rstudio Rstudio can not open a new rmarkdown file and it requests an updated version. However, when I tried to install one , it did not work. **Here is what I got:** Installing package into 'C:/Users/tmm447/Documents/R/win-library/3.3' (as ...
package updates rmarkdown written 15 months ago by tarek.mohamed0 • updated 15 months ago by James W. MacDonald45k
0
votes
1
answers
260
views
1
answers
Comment: C: topgo rnaseq error
... Hi , I knew what was the mistake. I have added gene names instead of ensembl gene id to my results, that is why the mapping did not work. Thanks Tarek ...
written 15 months ago by tarek.mohamed0

Latest awards to tarek.mohamed

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 2.2.0
Traffic: 153 users visited in the last hour