User: anoops

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anoops30
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5 days, 18 hours ago
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2 years, 1 month ago
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Posts by anoops

<prev • 8 results • page 1 of 1 • next >
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Comment: A: Plink2 Linear Regression for Binary phenotypes
... Thanks chrchang523. I understand this, I am however trying to analyze a large dataset compared my Computational resources and logistic regression is a lot more expensive. I will try the hack, thanks! ...
written 6 days ago by anoops30
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Plink2 Linear Regression for Binary phenotypes
... Hello, I am trying to run a GWAS with linear regression using Plink2. I call for linear however, the moment plink2 detects a binary phenotype it switches to logistic. Has any one else faced this issue? Is there a work around? Plink2: $plink2 --pfile $pfile \ --pheno $pheno_file \ ...
software error snp written 6 days ago by anoops30
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Comment: C: BAM to FASTQ picard or samtools
... That makes more sense now, I will try the sorting. Thanks! ...
written 2.1 years ago by anoops30
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Comment: C: BAM to FASTQ picard or samtools
... Sorry, did not realize. Will keep in mind. ...
written 2.1 years ago by anoops30
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Comment: C: BAM to FASTQ picard or samtools
... Good tip, thanks ATpoint ...
written 2.1 years ago by anoops30
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Comment: C: BAM to FASTQ picard or samtools
... Thank you h.mon. I see that the collate routine has the option to output primary alignments only. It seems like Picard is preferable for this purpose. Actually the read count is what triggered the problem, they both output the exact same number according to Fastqc. "Total Sequences : 49148031" in t ...
written 2.1 years ago by anoops30
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Comment: C: BAM to FASTQ picard or samtools
... I didn't include them because they were default. They are included now. Thanks in advance!!! ...
written 2.1 years ago by anoops30
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BAM to FASTQ picard or samtools
... Hello, I am trying to convert a batch of BAM files to FASTQs. I started out testing SAMTOOLS (collate/bam2fq) and PICARD (SAMTOFATQ). On the outset the numbers seemed OK but the statistics suggests that the SAMTOOLS out has twice the amount of duplicates as the Picard out. Has anyone experienced ...
assembly next-gen sequencing written 2.1 years ago by anoops30 • updated 2.1 years ago by h.mon31k

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Popular Question 2.1 years ago, created a question with more than 1,000 views. For BAM to FASTQ picard or samtools

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