User: chrisclarkson100

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Posts by chrisclarkson100

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Comment: C: uploading bigwig file (converted from BED) to UCSC genome browser: Unrecognized
... It looks like it did not recognize it as BigWig initially. After adding "type=bigWig" the mistake disappeared, thank you! ...
written 11 days ago by chrisclarkson10080
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Comment: C: uploading bigwig file (converted from BED) to UCSC genome browser: Unrecognized
... 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 11 days ago by chrisclarkson10080
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uploading bigwig file (converted from BED) to UCSC genome browser: Unrecognized format line 1
... 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 ...
software error assembly chip-seq written 11 days ago by chrisclarkson10080 • updated 10 days ago by ruisergioluis20
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Comment: C: MEME-Chip output lacks motif names
... 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 12 days ago by chrisclarkson10080
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Comment: C: MEME-Chip output lacks motif names
... @`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 12 days ago by chrisclarkson10080
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Am I correctly converting MotifDb PFMs to PWMs?
... 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) ...
pwm sequence pfm written 6 months ago by chrisclarkson10080
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Comment: C: trying to reproduce heat map made via cBioportal using download data
... 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 12 months ago by chrisclarkson10080
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Comment: C: trying to reproduce heat map made via cBioportal using download data
... thanks this has been amended ...
written 12 months ago by chrisclarkson10080
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Comment: C: trying to reproduce heat map made via cBioportal using download data
... Hi sorry forgot to add step about "clicking 'Heatmap>>Add genes to heatmap>>cluster heatmap". The question has been modified necessarily. ...
written 12 months ago by chrisclarkson10080
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trying to reproduce heat map made via cBioportal using download data
... 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& ...
rna-seq written 12 months ago by chrisclarkson10080 • updated 12 months ago by Kevin Blighe43k

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