User: Seigfried

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Seigfried70
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Posts by Seigfried

<prev • 38 results • page 1 of 4 • next >
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Comment: C: Barcode cross contamination
... [@genomax][1] I realised that as well. For a good sequencing run, I found that I discarded around 15% of the raw reads. However, after mapping with bowtie2, the difference in the mapping % was around 2% compared to the original sample and the number of mapped reads lost was also around 13% So basic ...
written 11 months ago by Seigfried70
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Comment: C: Barcode cross contamination
... @genomax Hello. Usually I have seen a typical trend of Qscores being quite high at the start of a read and then slowly dipping down at the end. We usually do a FastQC on the data as a standard Quality Control measure. In the current sequencing samples that I have, I see a Qscore going below 28 and s ...
written 11 months ago by Seigfried70
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Comment: C: Barcode cross contamination
... Thanks for the reply @gb. Yes I mean the same thing by 'barcodes' which are used to separate different species/samples. I have a set of 60 barcodes which supposedly permit specificity upto 2 mismatches and I wanted to test that. So I ended up writing a perl script to manually check quality scores of ...
written 11 months ago by Seigfried70
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Barcode cross contamination
... Dear all Is there any way to **remove** entire reads from a FastQ file IFF the first "x" bases are of bad quality? I will FastQC the whole read later for a cumulative score but right now I am interested in the barcode region. Basically I fear barcode contamination and I do not wish to keep the re ...
barcode trimming written 11 months ago by Seigfried70
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Comment: C: Getting a distinct set of Gene Ontology terms
... Thanks. I downloaded the available GO's from GO.db before this to remove some redundant GO's from DAVID. Found like 3 David GOs non-existent in GO.db ...
written 14 months ago by Seigfried70
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Answer: A: Getting a distinct set of Gene Ontology terms
... I tried using [Simplify][1] from ClusterProfiler and it seems to work although I need to explore the package to check how well it works. For now the results appear to be quite nice! [1]: https://guangchuangyu.github.io/2015/10/use-simplify-to-remove-redundancy-of-enriched-go-terms/ ...
written 14 months ago by Seigfried70
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Getting a distinct set of Gene Ontology terms
... Dear all I have a set of GO's with their corresponding NCBI-Entrez genes. A subset is as follows: GO:0005982 starch metabolic process 2875020:2875019:2868278:2874098 GO:0006559 L-phenylalanine catabolic process 2873317:2874818:2874819:2874820 GO:0006572 tyrosine catabolic process 28748 ...
gene ontology go written 14 months ago by Seigfried70
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Comment: C: Complex Heatmap subscripts
... Thank you and apologies! I got it to work in case i wanted multiple words in the subscript list(title = expression(log[hello~world]~Normalised~Values)) So I guess as usual [ ] denotes the start-end of the subscript. But I do not know why the tilde (~) is a substitute for a space [https://stackove ...
written 20 months ago by Seigfried70
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Comment: C: Complex Heatmap subscripts
... Well, for me it works with column_title and not with name. name = expression(log[2]~score), column_title = expression(log[2]~score), ...
written 20 months ago by Seigfried70
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Complex Heatmap subscripts
... Hello all I love the package 'Complex Heatmaps' to draw heatmaps in R and I quit using Heatmap.2. However in heatmap.2, I could use something like expression(paste) to get some words as subscripts. main = expression(paste("Log[2]","(FPKM) Values")) Unfortunately, expression doesn't seem to w ...
complex heatmap subscript written 20 months ago by Seigfried70

Latest awards to Seigfried

Scholar 13 months ago, created an answer that has been accepted. For A: Getting a distinct set of Gene Ontology terms
Popular Question 20 months ago, created a question with more than 1,000 views. For Heatmap.2 giving specific color to a value and start gradient after
Popular Question 20 months ago, created a question with more than 1,000 views. For How do i assign a kmer value?
Popular Question 20 months ago, created a question with more than 1,000 views. For Quake Error Corrector
Popular Question 20 months ago, created a question with more than 1,000 views. For R merge columns in the same file with identical column names and remove duplicates
Popular Question 2.3 years ago, created a question with more than 1,000 views. For ChIP-Seq TSS Line Plot

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