User: simplitia

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simplitia30
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2 years, 8 months ago
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Posts by simplitia

<prev • 18 results • page 1 of 2 • next >
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Help convert GDC exploration url to API download?
... Hi all, I have the search query from GDC https://portal.gdc.cancer.gov/exploration?cases_size=10000&facetTab=mutations&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.available_variation_data%22%2C%22value%22%3A%5B%22ssm ...
portal mutation gdc written 4 days ago by simplitia30 • updated 1 hour ago by Biostar ♦♦ 20
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Comment: C: How to recreate FASTQ from BAM
... this looks promising. I'm going try this and report back. Thanks. ...
written 7 days ago by simplitia30
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How to recreate FASTQ from BAM
... Hi all I been testing a paired RNA.seq sample. I start with a paired of FASTQ files and do alignment with STAR and run STAR-Fusion. Everything looks good until I try to reverse the BAM files generated from STAR originally to fastq and rerun STAR-Fusion; this resulted in about half the fusions tha ...
bam rna-seq sequencing written 7 days ago by simplitia30 • updated 7 days ago by ctseto20
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Comment: C: Converting large (compressed and unsorted) BAM files to fastq
... Hi Brian, so I tried this: reformat.sh in=test.bam out=stdout.fq | reformat.sh in=stdin.fq out1=r.1.fq.gz out2=r.2.fq.gz interleaved addcolon however, I've been getting this error message: Input is being processed as unpaired java.lang.AssertionError: TODO: Encountered a read with ' ...
written 5 months ago by simplitia30
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How to deconvolute whole blood and analyzed cell type separately for EWAS
... Hi I have whole blood CpG from the 850K EPIC plateform. My goal is to try understand how deconvolusion works; that is would it be possible separate out the cpgs into different subtype and run a EWAS for each cell type. separately? For example lets say I'm comparing group A to control using whole ...
epic methylation 850k cpg written 10 months ago by simplitia30 • updated 10 months ago by Kevin Blighe33k
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Comment: A: How to download raw sequence data from GEO/SRA
... Hi, how do we put in a dbgap crendentials? I tried: prefetch -v SRR617345 but I'm getting this error. err: query unauthorized while resolving tree within virtual file system module - failed to resolve accession 'SRR617345' - Access denied - please request permission to access phs000468/PCR in d ...
written 10 months ago by simplitia30
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Comment: C: How to quantify PCR duplication from bam file
... After searching around a bit the solution is to use samtools flagstat; this works for me in case someone else stumbles on to this thread. thanks. ...
written 11 months ago by simplitia30
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How to quantify PCR duplication from bam file
... Hi I know that I can mark and remove duplicate using picard. However is there way I can quantify how much duplication I have? So for example lets say I have file1.bam - mark and remove duplication resulting in file2.bam now what I like to do is quantify pcr duplication for file1.bam and file2.b ...
rna-seq written 11 months ago by simplitia30 • updated 11 months ago by genomax59k
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Comment: C: Hard time trying to calculate Allele Frequency and DP from Platypus
... yes its good to check, I think you mean NF + NR = TR ; thanks again, super helpful. ...
written 11 months ago by simplitia30
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Comment: C: Hard time trying to calculate Allele Frequency and DP from Platypus
... @Kevin Blighe: yes thank you I'm still new to handling VCF files and your question was enough to answer my question since the header already contained the info I needed which was defining what each of those mean. For allele frequency I think this would be TR / TC since the header reads INFO=I ...
written 11 months ago by simplitia30 • updated 11 months ago by Kevin Blighe33k

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