User: chrisclarkson100
chrisclarkson100 • 90
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Posts by chrisclarkson100
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... 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
chrisclarkson100 • 90
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... 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
chrisclarkson100 • 90
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... thanks yes that was a typo- corrected now
...
written 5 months ago by
chrisclarkson100 • 90
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... 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: ...
written 5 months ago by
chrisclarkson100 • 90
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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
chrisclarkson100 • 90
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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 19 months ago by
chrisclarkson100 • 90
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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 19 months ago by
chrisclarkson100 • 90
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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 19 months ago by
chrisclarkson100 • 90
• updated
19 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 19 months ago by
chrisclarkson100 • 90
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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 19 months ago by
chrisclarkson100 • 90
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