User: chrisclarkson100

Reputation:
80
Status:
Trusted
Location:
European Union
Last seen:
2 weeks ago
Joined:
5 years, 2 months ago
Email:
c***************@yahoo.co.uk

Posts by chrisclarkson100

<prev • 99 results • page 1 of 10 • next >
0
votes
2
answers
600
views
2
answers
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 6 months ago by chrisclarkson10080
0
votes
2
answers
600
views
2
answers
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 6 months ago by chrisclarkson10080
2
votes
2
answers
600
views
2
answers
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 6 months ago by chrisclarkson10080 • updated 6 months ago by ruisergioluis30
0
votes
1
answer
422
views
1
answers
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 6 months ago by chrisclarkson10080
0
votes
1
answer
422
views
1
answers
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 6 months ago by chrisclarkson10080
1
vote
0
answers
436
views
0
answers
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 12 months ago by chrisclarkson10080
0
votes
1
answer
704
views
1
answers
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 18 months ago by chrisclarkson10080
0
votes
1
answer
704
views
1
answers
Comment: C: trying to reproduce heat map made via cBioportal using download data
... thanks this has been amended ...
written 18 months ago by chrisclarkson10080
0
votes
1
answer
704
views
1
answers
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 18 months ago by chrisclarkson10080
1
vote
1
answer
704
views
1
answer
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 18 months ago by chrisclarkson10080 • updated 18 months ago by Kevin Blighe52k

Latest awards to chrisclarkson100

Popular Question 7 weeks ago, created a question with more than 1,000 views. For blastn linux command specify database
Popular Question 5 months ago, created a question with more than 1,000 views. For blastn linux command specify database
Centurion 6 months ago, created 100 posts.
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: The web page at ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra
Popular Question 9 months ago, created a question with more than 1,000 views. For blastn linux command specify database
Popular Question 10 months ago, created a question with more than 1,000 views. For blastn linux command specify database
Popular Question 10 months ago, created a question with more than 1,000 views. For blastn linux command specify database
Popular Question 12 months ago, created a question with more than 1,000 views. For blastn linux command specify database
Popular Question 12 months ago, created a question with more than 1,000 views. For blastn linux command specify database
Epic Question 13 months ago, created a question with more than 10,000 views. For what are single copy genes?
Popular Question 13 months ago, created a question with more than 1,000 views. For blastn linux command specify database
Epic Question 13 months ago, created a question with more than 10,000 views. For what are single copy genes?
Popular Question 17 months ago, created a question with more than 1,000 views. For blastn linux command specify database
Popular Question 17 months ago, created a question with more than 1,000 views. For blastn linux command specify database
Popular Question 18 months ago, created a question with more than 1,000 views. For blastn linux command specify database
Scholar 2.1 years ago, created an answer that has been accepted. For A: The web page at ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra
Popular Question 2.1 years ago, created a question with more than 1,000 views. For blastn linux command specify database
Supporter 2.2 years ago, voted at least 25 times.
Popular Question 2.3 years ago, created a question with more than 1,000 views. For blastn linux command specify database
Popular Question 2.4 years ago, created a question with more than 1,000 views. For blastn linux command specify database
Great Question 2.7 years ago, created a question with more than 5,000 views. For what are single copy genes?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For sequence BLASTed against itself.... why?
Great Question 2.8 years ago, created a question with more than 5,000 views. For venn diagram for gene lists using R
Popular Question 2.8 years ago, created a question with more than 1,000 views. For what are single copy genes?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For what are single copy genes?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1366 users visited in the last hour