User: chrisclarkson100
chrisclarkson100 • 80
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Posts by chrisclarkson100
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... It looks like it did not recognize it as BigWig initially. After adding "type=bigWig" the mistake disappeared, thank you! ...
written 6 months ago by
chrisclarkson100 • 80
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... Yes, I mean I am providing the link to my web site where the BiWig file is stored in the same way as you wrote. Here is the mistake that I get:
Unrecognized format line 1 of file: mywebsite/filename.bw (note: chrom names are case sensitive, e.g.: correct: 'chr1', incorrect: 'Chr1', incorrect: '1')
...
written 6 months ago by
chrisclarkson100 • 80
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... I have bed file data that was mapped with Bowtie 1 and the output of this was converted to bed files.
After having done my data analysis my lab need to upload the bed file data, in coverage format, to the UCSC genome browser i.e. the data are needed in 'bigWig' format.
So I went about converting t ...
written 6 months ago by
chrisclarkson100 • 80
• updated
6 months ago by
ruisergioluis • 30
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... I found out the answer to this question from : https://www.biostars.org/p/287257/
The following worked:
meme-chip -oc out -db motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme -db motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_redundant.meme seqs.fa ...
written 6 months ago by
chrisclarkson100 • 80
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... @`Gautier Richard`
Hi this is quite useful thank you however I am confused about specifying the database using the link that you supplied above:
meme-chip -oc out seqs.fa
The above takes a relatively short time but the discovered motifs lack names as mentioned in the question.
However when I ...
written 6 months ago by
chrisclarkson100 • 80
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... I apologise if some version of this question has already been asked in some way- I could not find any issues that were similar to my own.
I have a choice between taking data from the datasource package 'MotifDb' and 'JASPAR2018':
MotifDb has a much larger wealth of PFMs:
library (MotifDb)
...
written 12 months ago by
chrisclarkson100 • 80
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... Hi thank you. You're answer is certainly an improvement on mine.
![enter image description here][2]
https://ibb.co/giCkcy
**As for creating the histogram:**
head(data[,c(1:4)])
Hugo_Symbol Entrez_Gene_Id TCGA.3C.AAAU.01 TCGA.3C.AALI.01
1 LOC100130426 100130426 ...
written 18 months ago by
chrisclarkson100 • 80
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... thanks this has been amended ...
written 18 months ago by
chrisclarkson100 • 80
0
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... Hi sorry forgot to add step about "clicking 'Heatmap>>Add genes to heatmap>>cluster heatmap". The question has been modified necessarily. ...
written 18 months ago by
chrisclarkson100 • 80
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... I need to make a statistical comparison using breast cancer data. I have made a heat map at the following link on the Bioportal:
http://www.cbioportal.org/index.do?cancer_study_id=brca_tcga&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&data_priority=0&case_set_id=brca_tcga_mrna& ...
written 18 months ago by
chrisclarkson100 • 80
• updated
18 months ago by
Kevin Blighe ♦ 52k
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