User: ste.lu

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ste.lu60
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Posts by ste.lu

<prev • 48 results • page 1 of 5 • next >
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check co-occurrence of SNV/INDEL in a vcf file
... Hi All, I have an aggregate vcf file that has several samples and this structure: CHROM POS REF ALT SAMPLE1 SAMPLE2 ... SAMPLE_N chr1 10 A T 0/0 0/1 ...0/0 chr1 30 T C 0/0 0/1 ...0/0 chr1 60 G T 1/0 0/0 ...0/0 I would like to check compound heterozygosity in non-coding regions. I ...
genome assembly forum snp sequencing written 4 months ago by ste.lu60
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Comment: C: Extract samples from a bcf files based on genotype?
... Hi Pierre, Thanks a lot for your quick answer. Unfortunately, is note that easy to try it, I am working on HPC and they are quite strict about installing new packages. I'll try to git clone it. Thanks again. ...
written 8 months ago by ste.lu60
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Extract samples from a bcf files based on genotype?
... Hi All, I am looking for a way (possibly using bcftools) to extract samples based on the variant, but I haven't found it yet. For instance: CHROM POS REF ALT SAMPLE.A SAMPLE.B SAMPLE.C chr1 10 A ...
genome next-gen snp sequencing written 8 months ago by ste.lu60 • updated 8 months ago by chrchang5237.1k
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Comment: C: Identifying the orientation of a CTCF motif?
... Hello yztxwd, Thanks for your suggestions ...
written 9 months ago by ste.lu60
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Use arrows to indicate CTCF motifs orientation
... Hi All! I've used gimmemotifs tool to get the CTCF motifs orientation from a Chip-Seq experiment. I managed to colour code the bed file according to the motif strandedness (if the motif is on the positive or negative strand) and visualise them on IGV. I was wondering if anyone knows how to use arr ...
chip-seq sequencing written 9 months ago by ste.lu60
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Comment: C: Identifying the orientation of a CTCF motif?
... Even if an old answer, I am using it for my purposes. I want to have a final bed file with CTCF colour coded annotation according to the motif orientation on the genome. But I keep having problems with the code. I am using this command: ```gimme scan MK_CTCF_From_Romina_hg38_c10.0_l245_g100_peaks ...
written 10 months ago by ste.lu60
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Replication timing definition in Chip-Seq
... Hi there! I was wondering if anyone can help me out in a doubt I have about the calculation of the replication time. One can infer the replication time of the DNA by looking at the DNA amount of a region and compare it to the average of its chromosome. e.g. if I sequence Chromosome 1 and I see do ...
genome next-gen written 12 months ago by ste.lu60
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Comment: C: Extract Interaction Matrix from UpSetR
... Thanks for your answer. Do you know if there is a package (preferably in R) which I can implement in my script? ...
written 12 months ago by ste.lu60
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Extract Interaction Matrix from UpSetR
... Do you know if there is a way to extract the interaction matrix UpSetR is creating for its plots? I want to plot the interactions in between the columns of my data.frame, but I have several columns and UpSetR style of plotting is quite heavy. To solve this problem, I'd like to extract the values an ...
R interactions upsetr tool matrix written 12 months ago by ste.lu60 • updated 12 months ago by Alex Reynolds30k
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Looking for the best plot for overlapping features
... Hi All, I am looking for a way to plot a big spreadsheet of genomic features. The table has this structure: Promoter.id1 Promoter_flanking_region.id1 Enhancer.id1 FLI1.id1 GATA1.id1 GATA2.id1 TAL1.id1 CTCF.id1 Exons.id1 Intron.id1 0 0 0 ...
suggestion plot written 12 months ago by ste.lu60 • updated 12 months ago by RamRS28k

Latest awards to ste.lu

Popular Question 8 weeks ago, created a question with more than 1,000 views. For problem with HOMER findMotifsGenome.pl
Popular Question 4 months ago, created a question with more than 1,000 views. For Seqtk subseq: structure of file name.lst
Popular Question 4 months ago, created a question with more than 1,000 views. For Seqtk subseq: structure of file name.lst
Popular Question 17 months ago, created a question with more than 1,000 views. For Seqtk subseq: structure of file name.lst
Popular Question 19 months ago, created a question with more than 1,000 views. For Install Bowtie2 on Windows 10 Home edition

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