User: rrdavis

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rrdavis20
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United States
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17 hours ago
Joined:
4 years, 9 months ago
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Posts by rrdavis

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Normalization of virally infected human cells
... Here is a summary of the results table for one of the comparisons between activated and non-activated on read counts from human only. out of 27788 with nonzero total read count adjusted p-value < 0.05 LFC > 0 (up) : 4519, 16% LFC < 0 (down) : 380 ...
written 17 days ago by rrdavis20
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Comment: C: Normalization of virally infected human cells
... True. I see little counts before activation so like you said before and after activation differences on the viral side might not make sense. In an effort to keep things simple, I failed to say that I have one three conditions: one before activation and 2 conditions post activation ( these two cond ...
written 21 days ago by rrdavis20
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Comment: C: Normalization of virally infected human cells
... Thank you for your response. I will generate the MA-plots in DESeq2 for the host data and attach those here. If the MA-plots look typical, how should I proceed with the viral DGE? There are close to 100 genes in the viral genome. If the host data (MA plots look normal), Should I import the viral ...
written 21 days ago by rrdavis20
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Comment: C: Normalization of virally infected human cells
... Every sample was sequenced to the same depth. The drop I refer to is because the % of viral reads goes significantly up! ...
written 21 days ago by rrdavis20
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Normalization of virally infected human cells
... Hi, I have been given some RNA-seq data from a human cell line infected with a virus that can be activated. Upon activation, we see a large drop of reads mapping to the human genome (it goes from from ~75% to %40 upon activation). There is a large shift from human to virus expression upon activat ...
rna-seq written 21 days ago by rrdavis20
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Collapse duplicate rows and create new columns
... Hi, I have some data that looks like this in R: ## ID td yr mo dy ## 1 1 0 18 3 2 ## 2 1 1 17 3 12 ## 3 1 2 16 1 4 ## 4 2 2 18 3 7 ## 5 2 0 19 2 8 I have some duplicates in column ID (there are sometimes triplicates) and would like the outp ...
R written 8 months ago by rrdavis20 • updated 8 months ago by zx87548.8k
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Comment: C: How to compare coverage eveness of two whole genome sequencing runs of the same
... In this case which normalization method would you recommend for WGS ...
written 9 months ago by rrdavis20
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Answer: A: BWA mem paired end vs single end shows unusual flagstat summary
... Here is the output from BWA (version 0.7.15-r1140) in case it reveals something: [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 320216 sequences (80000259 bp)... [M::process] read 157448 sequences (39909865 bp)... [M::mem_pestat] # candidate unique pairs for (FF ...
written 2.9 years ago by rrdavis20
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Comment: C: BWA mem paired end vs single end shows unusual flagstat summary
... Thanks Devon for your input. I checked out the PE alignments in IGV, as you suggested, and noticed that there are small little clusters (~20 bp in length) of alignments with depth of 20000 reads for some of these clusters. Both read1 and read2 are overlapping in those clusters. IGV shows that th ...
written 2.9 years ago by rrdavis20
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Comment: C: BWA mem paired end vs single end shows unusual flagstat summary
... Out of the 307795 reads that map in the paired end analysis, 189907 reads have a mapQ >=5 (~61%). ...
written 2.9 years ago by rrdavis20

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Popular Question 2.9 years ago, created a question with more than 1,000 views. For BWA mem paired end vs single end shows unusual flagstat summary

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