User: woongjaej

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woongjaej10
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Posts by woongjaej

<prev • 30 results • page 1 of 3 • next >
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Comment: C: DESeq2 DEG analysis using different sequencing depth data
... Thank you h.mon for your kind replies! Woongjae ...
written 7 hours ago by woongjaej10
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Comment: C: DESeq2 DEG analysis using different sequencing depth data
... Sorry, I have misunderstood your comment. I'll try to ru your suggestion. Thanks ...
written 10 hours ago by woongjaej10
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Comment: C: DESeq2 DEG analysis using different sequencing depth data
... Hi swbarnes2 I perfomed differential expression analysis in two groups.(1. low depth samples 3 vs 3 deg analysis 2. high depth samples 4vs4) It seems there is no drastical difference, but the fdr of some genes have improved. For example, if I use just high depth samples to analysis deg, some gene ...
written 11 hours ago by woongjaej10
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Comment: C: DESeq2 DEG analysis using different sequencing depth data
... Hi h.mon! 1. Reads of high and low depth samples are about 100million and 10million reads each. 2. The library preparation of the samples were performed 2times. Like experiment 1, experiment2. Their designs are all same, only used sample is different(ex. tissue of different mouse, but same condit ...
written 12 hours ago by woongjaej10
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Comment: C: DESeq2 DEG analysis using different sequencing depth data
... Thanks goodez!! DESeq2 uses raw count number at the begining of the process. Maybe DESeq2 also uses similar method to normalize the raw counts.But I'm not sure of it and my data of two sequencing depth groups seems to have different FPKM and very different normalized count number. So I'm looking for ...
written 17 hours ago by woongjaej10
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DESeq2 DEG analysis using different sequencing depth data
... Hi, guys. I have a question analysing RNA-seq data(I'm using DESeq2) I'm willing to use **8 samples with high sequencing depth**, and **6 samples with low sequencing depth**.(About 4times lower). Can I use these data to analysis in DESeq2?? Does DESeq2 normalizes these samples' count for using?? ...
sequencing deseq2 rna-seq deg depth written 19 hours ago by woongjaej10 • updated 9 hours ago by h.mon20k
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qualimap transcript coverage profile truncated in smRNA-seq( ENCODE PIPELINE)
... Hi, guys. I'm processing some smRNA-seq data which are single-end data with STAR. (ENCODE PIPELINE guide line) But when I do QC with qualimap2 after the alignment, some samples get strange value or no values at the transcript coverage profile lines. (ex. absence or some weird value like 477) Does ...
qaulimap2 smrna-seq star written 3 months ago by woongjaej10
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Comment: C: sequencing of control sample in ChIP-seq??
... Thank Ryan for kind reply!! ...
written 4 months ago by woongjaej10
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sequencing of control sample in ChIP-seq??
... Hi guys, I'm trying to analysis ChIP-seq data and have a question about control sample. First, I sequenced my samples about 2 G bases to check the quality of the samples and libraries. I have verified samples' qualities and decided to sequence deeper for these samples. Assuming that I will read ...
chip-seq sequencing written 4 months ago by woongjaej10 • updated 4 months ago by Devon Ryan85k
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How to analysis 4c seq 3c seq data
... Hi, guys I have 3c seq fastq raw data. I searched how to analysis 3c seq data and got confused. I think basic analysis pipeline of 3c seq is different from other sequencings, right? For example, for other sequencing data, I first trim and QC the raw reads and get in to alignment with reference g ...
alignment 3c seq 4c seq written 6 months ago by woongjaej10

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