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Search: Posts Made By: IsmailM
Forum: Bioinformatics 09-08-2014, 01:56 PM
Replies: 2
Views: 2,798
Posted By IsmailM
BCL to FASTQ file converter bcl2fastq...

BCL to FASTQ file converter
bcl2fastq v02.14.01.07
Copyright (c) 2007-2013 Illumina, Inc.

This version has so many bugs in it. You should just upgrade to their new version 2.15. Also, which...
Forum: Bioinformatics 02-11-2014, 09:35 AM
Replies: 22
Views: 14,045
Posted By IsmailM
If you are using VarScan mpileup2snp or...

If you are using VarScan mpileup2snp or mpileup2indel, why does the QUAL column not have a number in it?
Forum: General 01-20-2014, 03:45 PM
Replies: 6
Views: 2,671
Posted By IsmailM
human transcriptome

check here for human mrna

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/
Forum: Bioinformatics 07-25-2013, 02:17 PM
Replies: 22
Views: 14,045
Posted By IsmailM
solved indel vcf format with awk command

Here is an awk command that can change your indel vcf format into the correct format.

cat Original_VCF | awk 'BEGIN {OFS="\t"} NR <= 24' > FINAL_VCF && cat Original_VCF | awk 'BEGIN {OFS="\t"} NR...
Forum: Bioinformatics 07-09-2013, 02:27 PM
Replies: 0
Views: 812
Posted By IsmailM
MultiCore Processing for CNVnator?

Hi all,

Is there a way to make CNVnator use multiple cores when it runs? I am on a 64 core Linux SGE running CentOS. I am on the partitioning step and it is taking a long time for one chromosome...
Forum: Bioinformatics 07-09-2013, 02:24 PM
Replies: 7
Views: 4,601
Posted By IsmailM
Multi-Thread CNVnator?

Hi all,

Is there a way to make CNVnator use multiple cores when it runs? I am on a 64 core Linux SGE running CentOS. I am on the partitioning step and it is taking a long time for one chromosome...
Forum: Bioinformatics 04-18-2013, 10:35 AM
Replies: 6
Views: 3,426
Posted By IsmailM
Try to add VALIDATION_STRINGENCY to your command.

Try to add VALIDATION_STRINGENCY to your command.
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