User: tarek.mohamed

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Posts by tarek.mohamed

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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 22 months ago by tarek.mohamed0
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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 22 months ago by tarek.mohamed0
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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 22 months ago by tarek.mohamed0
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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 22 months ago by tarek.mohamed0
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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 22 months ago by tarek.mohamed0
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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 22 months ago by tarek.mohamed0
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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 22 months ago by tarek.mohamed0 • updated 22 months ago by Wei Shi2.8k
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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 22 months ago by tarek.mohamed0 • updated 22 months ago by Wei Shi2.8k
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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 23 months ago by tarek.mohamed0 • updated 23 months ago by James W. MacDonald46k
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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 23 months ago by tarek.mohamed0

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