User: lauragouldgoetz

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Posts by lauragouldgoetz

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Answer: C: How to use 2 paired end .sam files in featureCounts?
... I just realized that I should have used the hisat2 command: hisat2 -x mm10/genome -1 fileName_1.fastq -2 fileName_2.fastq -S fileName.sam Then the resultant file goes on to featureCounts. Thank you for your help! ...
written 2.6 years ago by lauragouldgoetz10 • updated 2.6 years ago by Istvan Albert ♦♦ 82k
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Comment: C: How to use 2 paired end .sam files in featureCounts?
... The original .sra file fileName.sra was from paired reads. I first did: $ fastq-dump --split-files fileName.sra Then (on the two generated files: fileName_1.fastq and fileName_2.fastq): $ hisat2 -x mm10/genome -U fileName_1.fastq -S fileName_1.sam $ hisat2 -x mm10/genome -U fileName_2.fastq -S fil ...
written 2.6 years ago by lauragouldgoetz10
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How to use 2 paired end .sam files in featureCounts?
... Hello, I split paired ends data from RNA high throughput sequencing data into two .fastq and then .sam files (using fastq-dump, then hisat2) and want to put that data into featureCounts, but the only sample code I could find in their documentation references only one file. Does anyone know how I ca ...
alignment rna-seq sequencing written 2.6 years ago by lauragouldgoetz10 • updated 2.3 years ago by devbt1510

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