User: chrisclarkson100

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Posts by chrisclarkson100

<prev • 100 results • page 1 of 10 • next >
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Answer: A: tabix indexing a GTEx variant file- ':' delimited
... I proceeded as follows: import gzip import sys qtls=['sqtls','eqtls'] tissues=['Adipose_Subcutaneous', 'Adipose_Visceral_Omentum', 'Adrenal_Gland', 'Artery_Aorta', 'Artery_Coronary', 'Artery_Tibial', 'Brain_Amygdala', 'Brain_Anterior_cingulate_cortex_BA24', 'Brain_Caudate_basal ...
written 7 weeks ago by chrisclarkson10080
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Comment: C: tabix indexing a GTEx variant file- ':' delimited
... thanks yes that was a typo- corrected now ...
written 9 weeks ago by chrisclarkson10080
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tabix indexing a GTEx variant file- ':' delimited
... I have a gtex variant file- the head of which looks as follows: phenotype_id variant_id chr1:15947:16607:clu_36198:ENSG00000227232.5 chr1_13550_G_A_b38 ... chr1:15947:16607:clu_36198:ENSG00000227232.5 chr1_14671_G_C_b38 ... chr1:15947: ...
assembly next-gen snp written 9 weeks ago by chrisclarkson10080
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Comment: C: Convert SNPs from GrCh38 to 37
... I too am planning to do what's asked in the question. However I'm wondering- Is it possible that I may lose variants if I "lift backwards"? Hence is it best to always lift forwards?? Thanks in advance ...
written 12 weeks ago by chrisclarkson10080
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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 16 months 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 16 months 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 16 months ago by chrisclarkson10080 • updated 16 months ago by ruisergioluis30
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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 16 months 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 16 months 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 23 months ago by chrisclarkson10080

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Scholar 7 weeks 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 5 months ago, created a question with more than 1,000 views. For shiny giving spurious data-analysis output in comparison to non-shiny environment
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Popular Question 6 months ago, created a question with more than 1,000 views. For shiny giving spurious data-analysis output in comparison to non-shiny environment
Popular Question 6 months ago, created a question with more than 1,000 views. For blastn linux command specify database
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Popular Question 7 months ago, created a question with more than 1,000 views. For shiny giving spurious data-analysis output in comparison to non-shiny environment
Great Question 11 months ago, created a question with more than 5,000 views. For blastn linux command specify database
Popular Question 11 months ago, created a question with more than 1,000 views. For shiny giving spurious data-analysis output in comparison to non-shiny environment
Popular Question 11 months ago, created a question with more than 1,000 views. For blastn linux command specify database
Popular Question 11 months ago, created a question with more than 1,000 views. For Common match hit between 1st and 2nd round PSI BLAST
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Teacher 18 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
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