User: giulia.trauzzi

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Posts by giulia.trauzzi

<prev • 7 results • page 1 of 1 • next >
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Can I use FLEXBAR to detect and remove barcodes out of my short reads without demultiplexing ?
... Hello, I have demultiplexed my short reads and I have removed the Illumina adapter left in the sequences and now I need to remove the barcodes used by the sequencing centre from my reads. I have looked into Trimmomatic, Cutadapt (that I have used for the adapter removal) and FLEXBAR. As I have a ser ...
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Trimming Illumina Seq with TRIMMOMATIC
... Hello, I need to remove a common adapter and the barcode sequences from a bunch of samples (short reads - Illumina). I was able to remove the common adapter with cutadapt from all of the samples, however I would like to know how to use trimmomatic on single end reads to remove my barcode sequenc ...
trimmomatic illumina gbs written 13 days ago by giulia.trauzzi0
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Comment: C: Merging .fq files per sample using a big loop - BASH?
... Hi, thanks for your help. As I am a real beginner here, I struggle to understand the logic of the code. Also for each of my samples I have 3 or 4 files or 5 it changes throughout the batch, would the code still apply? I am running it on a copy of my samples. Thanks ...
written 18 days ago by giulia.trauzzi0
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Merging .fq files per sample using a big loop - BASH?
... Hi everyone! After demultiplexing my samples, I have 3 .fq files per sample (total of 720 samples) containing the raw reads. I managed to merge them in a merged files using this command line sudo cat PA001*.fq > PA001m.fq where my .fq files per sample are PA001.fq, PA001_1.fq, PA001_2.fq ...
loop fastq files merging samples genomics bash written 22 days ago by giulia.trauzzi0 • updated 22 days ago by lieven.sterck10k
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Mean sample depth?
... I am new to the SNP world and I am trying to understand the output of the SNP calling. I can't understand what the mean sample depth is. ...
snp depth written 26 days ago by giulia.trauzzi0
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Pairwise Fst values derived from different algorithms?
... Hello, I know that the Wright's Fixation Index (Fst) can range between 0 and 1 and for pairwise Fst is the same meaning that 0 two populations are not differentiated and 1 they are. I also noticed that the range can change from algorithm to algorithm used to generate the pairwise Fst values and i ...
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csv file format conversion to arp bash command line
... Hello, I have downloaded a free SNP dataset off the internet and I would like to run some population genetics analysis on it as practice. I managed to decompress the file on bash but now I need to convert the csv file into .arp that Arlequin can recognise. How can I do this on bash? Thanks ...
bash shell file conversion csv population genetics written 3 months ago by giulia.trauzzi0 • updated 3 months ago by GenoMax96k

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