User: MOJ

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MOJ0
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Posts by MOJ

<prev • 8 results • page 1 of 1 • next >
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Microarry (GSA) manifest file and CytoSNP-850K manifest file comparison
... How can I compare Microarry (GSA) manifest file and CytoSNP-850K manifest file? I want to know the commnon rsids in both the files. ...
snp written 23 days ago by MOJ0 • updated 23 days ago by curious450
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Comment: C: Microarry manifest file annotation
... I have .bpm file. The file contains following heading. > IlmnID Name IlmnStrand SNP AddressA_ID AlleleA_ProbeSeq AddressB_ID AlleleB_ProbeSeq GenomeBuild Chr MapInfo Ploidy Species Source SourceVersion SourceStrand SourceSeq TopGenomicSeq BeadSetID Exp_Clusters Intensity_Only RefStrand 1:1033803 ...
written 7 months ago by MOJ0
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Microarry manifest file annotation
... Can I annotate Illumina's Microarray manifest of file (GSA)? I tried with following steps: 1. Download Clinvar FTP from UCSC 2. Parse GSA file with the downloaded file. Kindly, let me know the feedback on the same I have also tried with SNPnexus. But could not since SNPnexus accepts only 100,000 SN ...
genome snp written 7 months ago by MOJ0 • updated 7 months ago by Biostar ♦♦ 20
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CYP2C19 variants with asterisk
... why the variants of CYP2C19 are indiacted with asterisk??? We have many genes in which SNPs lie within the same gene but are not represented by asterisk. ...
snp written 10 months ago by MOJ0
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Comment: C: Reference genome for WGS and WES.
... So tat means, hg38 need to be indexed for the alignment while Hg38gatkbundle need not as it has all the necessary files for alignment. ...
written 2.5 years ago by MOJ0
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Comment: C: RNAseq, indexing with STAR
... human.refseq.gff.gtf is 227M Genomic.fna is 3.1GB ...
written 2.5 years ago by MOJ0
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Comment: C: RNAseq, indexing with STAR
... When I used following command, several SA index files are generated. /path/to/star/STAR --runThreadN 2 --runMode genomeGenerate --genomeDir /path/to/star/genome_file --genomeFastaFiles /path/to/star/GCF_000001405.31_GRCh38.p5_genomic.fna --sjdbGTFfile /path/to/star/human.refseq.gff.gtf --sjdbOv ...
written 2.5 years ago by MOJ0 • updated 2.5 years ago by RamRS30k
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RNAseq, indexing with STAR
... I am wrking on RNAseq. I am using STAR for indexing. It generates all the files except the genome file.I am running the command on 30G RAM and 400G hard disk and 2 runthread. It took 2 days and is still running. Any opinion will be appreciated ...
rna-seq written 2.5 years ago by MOJ0

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Popular Question 8 months ago, created a question with more than 1,000 views. For RNAseq, indexing with STAR

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