User: chrisclarkson100

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Posts by chrisclarkson100

<prev • 101 results • page 1 of 11 • next >
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Answer: A: Error when using Bedtools fisher on sorted bed files
... I too have had this problem- but what has helped me is to sort the mm9.genome file with the same code as in the case of the actual bed files: sort -k1,1 mouse.mm9.genome > sorted_mouse.mm9.genome sort -k1,1 -k2,2n a.bed > a_sorted.bed sort -k1,1 -k2,2n b.bed > b_sorted.bed ...
written 5 weeks ago by chrisclarkson10090
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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 4 months ago by chrisclarkson10090
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Comment: C: tabix indexing a GTEx variant file- ':' delimited
... thanks yes that was a typo- corrected now ...
written 5 months ago by chrisclarkson10090
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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 5 months ago by chrisclarkson10090
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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 5 months ago by chrisclarkson10090
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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 19 months ago by chrisclarkson10090
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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 19 months ago by chrisclarkson10090
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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 19 months ago by chrisclarkson10090 • updated 19 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 19 months ago by chrisclarkson10090
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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 19 months ago by chrisclarkson10090

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