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User: daniel.soronellas

gravatar for daniel.soronellas
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Posts by daniel.soronellas

<prev • 53 results • page 1 of 6 • next >
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A couple of questions related to transcriptome assembly (Using Cufflinks/Scripture)
... Dear community, I performed a polyA+ stranded RNAseq experiment which I processed throught TopHat-Cufflinks and TopHat-Scripture in order to make a genome-guided transcriptome assembly, as was published in 2011 by Cabili et. al.. Therefore, I wanted to know If there's any tool/program to compute su ...
rnaseq cufflinks scripute lncrna written 3.8 years ago by daniel.soronellas • 330
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Comment: C: Efficiently join paired-end read coordinates in the same line?
... Thank you! Worked fine! ...
written 4.0 years ago by daniel.soronellas • 330
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Efficiently join paired-end read coordinates in the same line?
... Dear community, I have a huge paired-end HiC dataset (BAM format) which I want to format like this way: HWI-D00283:117:C5KKJANXX:2:1101:1139:77789 chr6 153338506 153338556 37 + chr6 153338031 153338081 37 - HWI-D00283:117:C5KKJANXX:2:1101:1139:77856 chr6 149915 ...
3c paired-end hic 4c written 4.0 years ago by daniel.soronellas • 330 • updated 23 months ago by Biostar ♦♦ 20
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Comment: C: PRIDE Mass-Spec Published data analysis?
... Didn't found anything about this topic yet, sorry! ...
written 4.1 years ago by daniel.soronellas • 330
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PRIDE Mass-Spec Published data analysis?
... Dear Community, I would like to know what are your recommendations in order to re-analyze (learn) the following already published MS data, from the paper: "Endogenous Purification Reveals GREB1 as a Key Estrogen Receptor Regulatory Factor", in PRIDE database. In order to learn how to process this k ...
mass-spect written 4.1 years ago by daniel.soronellas • 330 • updated 4.1 years ago by Laurent • 1.6k
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Where to download In-vitro RNA-seq published experiments?
... Dear all, I have a newbie question, basically where I can find published experiments of in-vitro polyA+ strand-specific RNA-seq samples from mainly cancer cell lines? FASTQ raw is fine enough to go on.  Thanks for your help!   ...
rna-seq written 4.2 years ago by daniel.soronellas • 330 • updated 4.2 years ago by Jelena Aleksic • 900
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Methods to subset sequenced experiments to account for differences in read counts?
... Hi All, I'm looking for advice and also to know what people usually do to account for differences between different sequenced experiments. For example if you have 2 ChIP-seq/RNA-seq/... experiments, one with 60M reads and the other with 40M reads, how do you obtain: 1.- BAM/SAM/BED file with the s ...
genome down-sampling sequencing written 4.4 years ago by daniel.soronellas • 330 • updated 4.4 years ago by mikhail.shugay ♦ 3.3k
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Comment: C: Large BAM file to GRanges object and then save as RData
... Thanks for your answer Michael, I know that R is not the best environment for this but the purpose of my analysis need to pass throught this step. Just one question: when you load your 21GB BAM file did you vary your code compare to mine? I want to know if I'm missing something, thanks!! ...
written 4.6 years ago by daniel.soronellas • 330
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Large BAM file to GRanges object and then save as RData
... Hi all, I have several BAM files which I would like to work in R environment. This are big files with more than 100M reads each. Is there any way to convert them in GRanges object and then save it as RData compressed file? So far what I've tried is the following Rcode:   library(GenomicRanges) l ...
rdata R bam granges object written 4.6 years ago by daniel.soronellas • 330
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Answer: A: Computational Validation Of Chip-Seq Peaks
... I think I came up with a possible solution to this: First find the peaks, whatever number you could obtain with a certain stringent cut-off (i.e. pvalue < 10e-5 and FDR < 1%). Get peak summits and make a window of 100 bp around the center. Then compute complementary regions (background) usin ...
written 5.1 years ago by daniel.soronellas • 330

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