User: P.NJ

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P.NJ50
Reputation:
50
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New User
Location:
Germany
Last seen:
4 years, 10 months ago
Joined:
8 years, 1 month ago
Email:
n*********@hotmail.com

Posts by P.NJ

<prev • 15 results • page 1 of 2 • next >
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Comment: C: GEO datasets for the eqtl analysis
... no I do not have access to dbGAP, I am using eqtl datasets available online ...
written 4.8 years ago by P.NJ50
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GEO datasets for the eqtl analysis
... Hello, How can I extract all datasets from GEO relating to Alzheimer's samples from GEO for eqtl analysis ?   Thank you ...
geo extract eqtl written 4.9 years ago by P.NJ50
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Comment: C: bam file readgroup to include several individuals
... Thanks but now it ends up adding everything in just one line several times: @RG ID:Library1 SM:NA19NA20NA21NA22... PL:Illumina LB:lib_2x250 DS:hg19 @RG ID:Library1 SM:NA19NA20NA21NA22... PL:Illumina LB:lib_2x250 DS:hg19 .. What I intended was @RG ID:Library1 SM:NA19 PL:Illumina ...
written 5.0 years ago by P.NJ50
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Comment: C: bam file readgroup to include several individuals
... Thank you... I understand the iteration part of it but I did not get the point: "(presumably you have path information in the samples.txt file)." So, what I have is only one library of pooled samples that contain both cases and controls (200 in total). The sample list is only the ID names in one co ...
written 5.0 years ago by P.NJ50
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bam file readgroup to include several individuals
... I have paired-end reads (gene-regions-exons) that contains 200 individuals and I want to include all the sample names in the read group. I have a text file in a single column and tried to include the readgroup when aligning file=($(cat samples.txt)) bwa mem -M -R "@RG\tID:Library1\tSM:$file\tPL:Il ...
readgroup split bam files bam file written 5.0 years ago by P.NJ50 • updated 5.0 years ago by Devon Ryan92k
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Comment: C: BWA or SMALT mapping algorithm
... what would be an alternative then ? ...
written 5.0 years ago by P.NJ50
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Comment: C: Parameters for BWA aln
... To explain it in simple words, DNA samples from cases and controls are combined together to form a population library and processed to produce sequence data for the defined target regions in the genes...  any suggestions for my questions ? ...
written 5.0 years ago by P.NJ50
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BWA or SMALT mapping algorithm
... I am using BWA for aligning targeted 'gene-pooled' exonic gene regions generated from Illumina 1.9 against whole genome human reference. The parameters I used for the command "aln" are  bwa aln -n 2 -q 15 -l 35 -t 8 -I But I was just wondering if it is a good idea to disable the seeding and also ...
smalt 2x250bp illumina reads bwa written 5.0 years ago by P.NJ50
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Comment: C: Concordance Using Plink
... well there is an in house tool which can convert SNPs into PLINK format. For the array data I used the lgen format. The SOLiD SNPs are names with the rs ids. i checked the bim files as well, the snps are in the form of rs ids and some of them are in this format : snp1_554484 ...
written 8.1 years ago by P.NJ50
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Answer: A: Converting Illumina Raw Genotype Data Into Plink Ped Format
... I would like to know if I am converting Illumina 2.5M array into plink, as the output should I not get approx 2-2.5M of SNPs ? I am getting approx 1M SNPs... does this happen ? ...
written 8.1 years ago by P.NJ50

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Popular Question 8.0 years ago, created a question with more than 1,000 views. For Converting Illumina Raw Genotype Data Into Plink Ped Format

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