User: MAPK

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MAPK1.1k
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Posts by MAPK

<prev • 354 results • page 1 of 36 • next >
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Comment: C: What are the major differences between plink and plink2?
... I was creating .bed file using `inputfile.ped` and `inputfile.map`. I was able to do it with plink, but not with plink2. What could be the reason? ...
written 1 day ago by MAPK1.1k
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Comment: C: What are the major differences between plink and plink2?
... Even this command doesn't work: `plink2 --file inputfile --make-bed --out outputfile` ...
written 1 day ago by MAPK1.1k
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What are the major differences between plink and plink2?
... Hi, I was running plink(1.9) tool to create bed file (`plink --file inputfile --make-bed --noweb --out outputfile`) which worked fine, but when I switched to plink2, the same command doesn't work. Can we do everything that plink(1.9) does with plink2? Can someone please clarify this? Thank you. ...
plink written 1 day ago by MAPK1.1k
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Comment: C: How can I calculate the number of sequences starting with different nucleotides
... Thank you so much. How do I get the sorted values in the table (shortest to longest sequence length)? ...
written 9 days ago by MAPK1.1k
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How can I calculate the number of sequences starting with different nucleotides using perl
... I am not familiar with perl (I mostly work with R) and I was hoping someone would help me with this problem. I have this test.fasta file below. I need to get this table from this fasta file where I have sequence length starting from minimum sequence length to maximum sequence length. Then I want to ...
fasta perl written 9 days ago by MAPK1.1k • updated 9 days ago by Neilfws47k
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How do I normalize this data for plotting?
... Hi, I am sorry for asking this silly question, but I am really confused with the normalization of this data set. I have three fastq files for RNAseq data. I have sampleA, sampleB and sample C. Suppose, the total reads in sampleA = 5 millions, sampleB = 7 millions and sampleC = 8 millions. Now, I hav ...
normalization written 9 days ago by MAPK1.1k • updated 9 days ago by shenwei3563.4k
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Comment: C: How do I extract aligned reads from BAM file?
... Thanks Devon. Since I will be extracting all the aligned reads from bam file, I had to use this command: `samtools fasta input.bam -F 4 > output.fasta` ...
written 10 days ago by MAPK1.1k
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How do I extract aligned reads from BAM file?
... Hi, I have a fasta sequence to which I have aligned a fastq file using bowtie and got a BAM file. I need to extract all the reads in fastq file that aligned to my fasta sequence. Can I just extract all the reads from the BAM file I got from bowtie alignment in this case? Please suggest me if I shoul ...
fastq bam written 10 days ago by MAPK1.1k • updated 10 days ago by Devon Ryan76k
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Comment: C: How can I plot alignment between fastq reads and reference sequence?
... Got it. Thank you so much. ...
written 14 days ago by MAPK1.1k
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Comment: C: How can I plot alignment between fastq reads and reference sequence?
... Thank you Sean for your answer. So for the first step, should I just extract the aligned bam file from bowtie alignment? ...
written 14 days ago by MAPK1.1k

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