User: Zee_S

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Zee_S50
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Posts by Zee_S

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Comment: C: how to visualize rna-seq coverage track in igv?
... Hello! I would like to come back to this post to ask: when we visualise RNA-seq tracks, do you include both unique and multi mappers? or why is it that some people only use unique mappers? which is the correct way? Thank you! ...
written 11 weeks ago by Zee_S50
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Comment: C: how to visualize rna-seq coverage track in igv?
... this is very useful feedback thank you very much. ...
written 6 months ago by Zee_S50
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Comment: C: how to visualize rna-seq coverage track in igv?
... what do you mean by larger zoom out? can you please elaborate? ...
written 7 months ago by Zee_S50
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how to visualize rna-seq coverage track in igv?
... Hello biostars community, how does one visualize an rna-seq coverage track alongside chip-seq bigwig tracks in igv? the problem i have is that, when i zoom into the rna-seq coverage track (becaus eit is a bam file), i lose the resolution on my bigwig tracks (too zommed in) and i can no longer vis ...
normalization bam coverage rna-seq igv written 7 months ago by Zee_S50 • updated 6 months ago by jared.andrews075.5k
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STAR mapping statistics don't add up with samtools count
... Hello Biostars community, I have PE samples mapped with STAR and i want to count the number of uniquely mapped reads using samtools. i did the following (using the Alex Dobin's advice in this link: https://groups.google.com/forum/#!topic/rna-star/pQbqeQd0lNY) : SE: $ samtools view -c -q 255 -F ...
read count pe samtools star se written 7 months ago by Zee_S50 • updated 7 months ago by lieven.sterck7.8k
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what does the alignment statistics of your RNA spike-in tell you about your sample of interest in two experimental conditions?
... Dear Biostars community, I was hoping to get your ideas on how to interpret RNA-seq data in two samples before and after drug treatment, based on the mapping statistics of exogenous spike-in RNA. One sample is untreated. the other sample is treated with a drug to (theoretically) increase transcrip ...
spike-in rna-seq normalization star written 7 months ago by Zee_S50
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Comment: C: Is there a way to get multiBigwigSummary with 1-based coordinates instead of 0-b
... understood. thank you so much for your help! ...
written 8 months ago by Zee_S50
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Comment: C: Is there a way to get multiBigwigSummary with 1-based coordinates instead of 0-b
... hi JC, thanks a lot for your answer. How exactly do i do that? i was thinking that if i modify the multi bigwig coordinates to 1-based, the score in column 4 that was calculated for the original 0-based coordinate will no longer be valid (since now the 1-based causes the bin to shift by 1 base pair ...
written 8 months ago by Zee_S50
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Is there a way to get multiBigwigSummary with 1-based coordinates instead of 0-based?
... Dear Biostars commmunity, I am seeking your advice to know if there is a way to overlap chip-seq scores distributed across 0-based consecutive genomic bins (generated by Deep tools multiBigwigSummary) onto expression scores generated for RNA-seq data distributed in similar consecutive genomic bins, ...
deeptools multibigwigsummary written 8 months ago by Zee_S50
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Comment: C: is 0-based start and 1-based end of bed format not compatible with htseq-count?
... got it! thank you so much! your explanations are very helpful for me to understand the logic of many analyses that i do with this program. ...
written 8 months ago by Zee_S50

Latest awards to Zee_S

Popular Question 6 months ago, created a question with more than 1,000 views. For How to add a regression line and change colors in ggplot smoothscatter?
Popular Question 6 months ago, created a question with more than 1,000 views. For How to do correlation analyses between RNAseq and ChIPseq library?
Popular Question 6 months ago, created a question with more than 1,000 views. For How to annotate repeats?
Popular Question 8 months ago, created a question with more than 1,000 views. For how to split/ expand a bedGraph file into genomic coordinates of equal bin size ?
Popular Question 17 months ago, created a question with more than 1,000 views. For how to split/ expand a bedGraph file into genomic coordinates of equal bin size ?

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