User: eoin

gravatar for eoin
eoin30
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New User
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Last seen:
4 months, 4 weeks ago
Joined:
2 years, 8 months ago
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e***@ualberta.ca

Posts by eoin

<prev • 5 results • page 1 of 1 • next >
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Ensembl assembly choice for RNA-Seq reference mapping
... Hello, Just a general question regarding choice of assembly version for RNA-Seq mapping. I have a bos taurus RNA-seq dataset, and my pipeline uses STAR for reference assembly alignment with featureCounts to count the genes. End goal is differential gene expression analysis, GO/Pathway etc. The S ...
ensembl alignment star rna-seq assembly written 7 months ago by eoin30 • updated 7 months ago by genomax75k
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Splitting a fasta file on the basis of header barcodes
... Hi folks, Having a bit of a brain fart, I'm sure there's a very simple solution to this: I have a fasta file containing reads from 48 different samples, and containing a barcode in the header line: >10_13 M01383:135:000000000-A7LW3:1:1101:16875:1408 1:N:0:1 orig_bc=GTACATACCGGT new_bc=GTACA ...
fasta dna-seq rna-seq written 2.4 years ago by eoin30 • updated 2.4 years ago by glihm610
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Comment: C: Question: Mean and SD read length from a range of fastq files
... Perfect. thank you so much. I had tried a loop but left out echo thanks a lot ...
written 2.7 years ago by eoin30
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Comment: C: Question: Mean and SD read length from a range of fastq files
... thank you for your answer Pierre!! This code will give us the total number of reads, their mean, and SD. But i think I wasn't clear in my post; what I need is to get the mean and SD read length from each *individual* .fastq file within in the directory. So an example of the output - File Name M ...
written 2.7 years ago by eoin30
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Question: Mean and SD read length from a range of fastq files
... Hi all, I'm trying to write some code to generate mean read length data from a range of fastq files. awk '{if(NR%4==2) print NR"\t"$0"\t"length($0)}' HG1.fastq > readLength.txt i've got as far as here from looking through other posts and trying to improve but i'm stuck on a couple of things. ...
fastq awk sed sequencing written 2.7 years ago by eoin30 • updated 14 months ago by savscosta0

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Popular Question 2.1 years ago, created a question with more than 1,000 views. For Question: Mean and SD read length from a range of fastq files
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Splitting a fasta file on the basis of header barcodes

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