User: simplitia

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simplitia30
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Posts by simplitia

<prev • 24 results • page 1 of 3 • next >
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How to interpret exon reads from recount for version 2?
... Dear all, I'm trying to get exon by exon data matrix. I can download the data either directly from the website or through the R package. For example here is simple single sample example: download_study("DRP001219", type = "rse-exon", outdir="./data/") load(file.path( "./data/rse_exon.Rd ...
tcga rna-seq written 9 days ago by simplitia30
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Answer: A: SOAPfuse: problem in constructing database
... Hi so I had the same issue and here is what I did to fix it. 1. You need to make sure that the fasta is indeed prefix with chr which you did above by checking. I mentioned this in case some else downloaded from ensembl which does not. You can easily check this by grepping the fasta, > grep " ...
written 7 weeks ago by simplitia30
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Advice for gene overlap with direction between two sets.
... Hi so I have a scenario where I have 200 samples. Each samples I test for 10000 genes. I have two events, call it A and B. Whereby for each sample there can be x genes with gene.up and gene.down. What I want to do is compare if events A and B are similar: I want to see if the intersection is sig ...
R chisquare statistics written 3 months ago by simplitia30
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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 5 months 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 6 months ago by simplitia30 • updated 6 months ago by kristoffer.vittingseerup2.2k
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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 7 months 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 8 months ago by simplitia30 • updated 6 months 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 8 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 8 months ago by simplitia30 • updated 8 months ago by ctseto70
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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 14 months ago by simplitia30

Latest awards to simplitia

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Create fusion transcripts with breakpoint coordinates from two genes.
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Hard time trying to calculate Allele Frequency and DP from Platypus

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