User: abdul.karim

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Posts by abdul.karim

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Comment: C: Clustering DNA sequences (from human genome)
... Yes, I am working on human genome (as a reference). And I have DNA reads from let's say two samples (two different individuals) and my goal is to cluster those DNA reads from two samples. Ideally, I should get two clusters using kmeans or any other algorithm. The first challenge is that reads are mo ...
written 6 months ago by abdul.karim0
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Comment: C: Clustering DNA sequences
... let's say I map my reads from two samples to a reference genome (either exact mapping or approximate mapping). If we assume that 60% of my reads from one sample (Sample-A) maps to the reference while 40% do not match. Now do you suggest that I take these 40% unmatched reads? I do the same for Sample ...
written 6 months ago by abdul.karim0
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removing duplicate sequences while extarcting the reads from fastq.gz
... I can extract the reads from fastq.gz file as follows. gunzip -c in.fastq.gz | awk '(NR%4==2)' > out.seq Is there anyway, that I only extract the unique reads and discard any duplicate reads? ...
genome sequence sequencing written 6 months ago by abdul.karim0 • updated 6 months ago by swbarnes27.5k
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Distance computation in Bio.Cluster
... I have sequence data in the form of a matrix as follows. matrix= [ [78 65 78 ... 84 65 65] [78 71 78 ... 71 71 71] [78 67 78 ... 84 65 84] ... [65 65 65 ... 65 65 71] [67 67 71 ... 84 65 65] [65 71 65 ... 65 65 84] ] The shape of this matrix is (105 ...
cluster bio.cluster biopython dna written 6 months ago by abdul.karim0
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extracting DNA sequnces from multiple fastq.gz files
... I have raw DNA sequences in multiple files as under. xxxxxx1.R1.fastq.gz xxxxxx2.R1.fastq.gz xxxxxx3.R1.fastq.gz xxxxxx4.R1.fastq.gz xxxxxx5.R1.fastq.gz I can extract the DNA raw reads from a single file and can store it in another file by using the following command. ...
gene raw_read_dna sequence multi_file sequencing written 6 months ago by abdul.karim0 • updated 6 months ago by h.mon29k
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Clustering DNA sequences (from human genome)
... Hi, I am very new to Genomics and to the DNA clustering specifically. I have around 100 samples with each having millions of DNA Reads. I used some sequence clustering method to make clusters for a single sample. But i think, clustring the millions of DNA reads of a single sample does not make an ...
genome sequencing written 6 months ago by abdul.karim0
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Extatrcting only sequnces from fastq.gz
... I have a fastq.gz file which contains millions of DNA sequences. IS there fast way to extract only the sequences (one sequence/read per line) and save all the sequences into csv or text file for further analysis? ...
rna-seq sequencing written 6 months ago by abdul.karim0 • updated 6 months ago by Pierre Lindenbaum127k
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Comment: C: ways to concatenate individual DNA sequences together to form complete sequence
... Thank you for the help. Would you please explain what is reference genome? by aligning, do you mean that I compare each of the read with the reference genome? ...
written 6 months ago by abdul.karim0
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ways to concatenate individual DNA sequences together to form complete sequence
... Hi, I am very new in the field of Genomics. So I apologize for a very basic question I am about to ask. I have raw DNA sequences for many samples. For a single sample, the DNA seq is chopped into fixed sized fragments and stored in FASTQ format. For instance, sample A DNA sequence is chopped into ...
gene assembly rna-seq sequencing written 6 months ago by abdul.karim0 • updated 6 months ago by swbarnes27.5k

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