User: msameet

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msameet30
Reputation:
30
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New User
Location:
United States
Last seen:
1 year, 8 months ago
Joined:
4 years, 8 months ago
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m******@gmail.com

Posts by msameet

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Subsetting Granges based on its metadata
... Another handy trick is to use the column name of the metadata directly. e.g. `all.vcf[(elementMetadata(all.vcf)[, "Name"] %in% filt.ids)]`. ...
written 21 months ago by msameet30
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Comment: C: Pheatmap Annotation
... It seems to be working just okay on Mac OS X. ...
written 3.2 years ago by msameet30
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Comment: C: Select sequences from fastq.gz file
... Hi, do you have any estimates on time taken? ...
written 4.3 years ago by msameet30
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Comment: C: Select sequences from fastq.gz file
... Yes, that worked. Thanks. ...
written 4.3 years ago by msameet30
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Comment: C: Select sequences from fastq.gz file
... This gives the following error sh ~/downloads/bbmap/reformat.sh in=../S11-12810Ca_005_ACAGTG_L001_R1_V2.fastq.gz out=sampled_S11-12810Ca_V2.fastq.gz reads=72000000 java -ea -Xmx200m -cp /ycga-ba/home/sm2556/downloads/bbmap/current/ jgi.ReformatReads in=../S11-12810Ca_005_ACAGTG_L001_R1_V2.fastq.gz ...
written 4.3 years ago by msameet30
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Comment: C: Select sequences from fastq.gz file
... No, I dont want to extract the files.  I saw the question, it assumes that the files are "extracted", no longer a *.gz. ...
written 4.3 years ago by msameet30
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Select sequences from fastq.gz file
... Is there a way to sample sequences from the `fastq.gz` file?  I have files that contain hundreds of millions of reads, I want to sample about 100 million reads from each file.  Is there a way to do this? ...
random selection fastq.gz select written 4.3 years ago by msameet30 • updated 4.3 years ago by Peter5.8k
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Problem with FPKM values
... I recently did a cuffdiff to estimate differential expression under two different conditions.  I did not have replicates for the data-sets.  I used tophat2 and cuffdiff2 for alignment and differential expression respectively.  However, most strangely, when I viewed the alignment on IGV, I can see fo ...
interpretation fpkm interpretaion written 4.7 years ago by msameet30 • updated 4.7 years ago by swbarnes25.0k

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Popular Question 3.1 years ago, created a question with more than 1,000 views. For Select sequences from fastq.gz file

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