User: simplitia

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simplitia30
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Posts by simplitia

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Understanding FANTOM5 CAGE fields
... great thanks that is super helpful. Here is couple of followup questions. 1. So using that example above, p1@LINC200277 is about 29 bp in width. So does that mean the TSS for this gene can be within any of the 29 bp in this range? 2. Moreover if its range how is it only a single digit 0bp_to_ ...
written 4 weeks ago by simplitia30
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Understanding FANTOM5 CAGE fields
... Hi recently I downloaded data from FANTOM5 Phase 2.0 ( http://biomart.gsc.riken.jp/ ) with the goal of figuring out TSS sites, however I cannot seem to find any documentations on this. For example, I downloaded FANTOM5 Phase 2. I'm a bit confused, ![enter image description here][1] [1]: http ...
transcription rna-seq tss written 4 weeks ago by simplitia30 • updated 4 weeks ago by kristoffer.vittingseerup1.6k
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Comment: C: from .BAM to .BAI using samtools
... thanks this is useful. Do you know what is the optimal way of setting -j ? Without setting it does it just default to max cores? Or should I set it to something total core minus 1. That is if I have 8 then I will just set it to 7? thanks. ...
written 11 weeks ago by simplitia30
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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 3 months ago by simplitia30 • updated 8 weeks 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 3 months 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 3 months ago by simplitia30 • updated 3 months 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 9 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 13 months ago by simplitia30 • updated 13 months ago by Kevin Blighe39k
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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/ ...
written 13 months ago by simplitia30 • updated 9 weeks ago by RamRS20k
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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 14 months ago by simplitia30

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