User: ste.lu

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ste.lu40
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Posts by ste.lu

<prev • 39 results • page 1 of 4 • next >
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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 5 days ago by ste.lu40 • updated 4 days ago by RamRS22k
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Bedtools shift in a defined chromosomal position
... Hi All! Do you know if there is a way to use bedtools shift tool in a defined chromosomal postions. In other words, shift +10 bp only the regions that are on chr1 in beteween 1 and 10000. E.g: chr1 10 100 chr1 20000 21000 bedtools shift -s 10 -chr_reg chr1:1-10000 chr1 20 110 c ...
bedtools written 5 weeks ago by ste.lu40 • updated 5 weeks ago by Pierre Lindenbaum121k
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Segment the genome in an unbiased way
... Hi there! I am analysing Hi-C experiments and I'd like to annotate the genome (i.e. Enhancers, promoters, exons, introns, intergenic regions) in an unbiased way. I'd like to keep record, in the annotation file, of the genomic features preceding the one I am considering. For instance, discriminate i ...
genome hi-c sequencing written 9 weeks ago by ste.lu40
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Comment: C: Visualize BEDPE file
... I was trying to use Rcircos and BioCircos, But I think I can't zoom in as much as I want, in terms of chromosomal region. Is it different for Circos? ...
written 6 months ago by ste.lu40
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Visualize BEDPE file
... Hi All, I have a bedpe file resulting from an HiC experiment. the structure is like this: `Chr_bait \t Start_bait \t End_bait \t Chr_target \t Start_target \t End_target \t Notes \t Stat_value` Currently I am visualising them on IGV and they looks likes arches that link the 2 regions (Bait to Ta ...
bed hic igv written 6 months ago by ste.lu40
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Comment: C: Group and merge entries in a table according to a second one
... Bedtools was the easier!! bedtools intrestect -a table1 -b table2 -wa > table3 and then filter table 3 for the repetitive entries awk '!a[$0]++' table3 ...
written 7 months ago by ste.lu40
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Group and merge entries in a table according to a second one
... Hi All, I have two tables so structured: Table1: chr1 1 16007 8899 chr1 16008 24571 294334 chr1 24572 27981 192966 chr1 27982 30429 708562 chr1 30430 32153 610786 chr1 32154 32774 837824 chr1 32775 37752 177990 ch ...
R next-gen assembly written 7 months ago by ste.lu40
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Comment: C: from GWAS to variants
... But how can I select the SNPs for a trait? ...
written 7 months ago by ste.lu40
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from GWAS to variants
... Hi All, Are you aware of a database or a way to help me in this task: Given a set of ~100 GWAS, how can I collect all the lead and tag SNPs called in these studies and merge them in a big tsv? What I've done so far was download from EBI GWAS catalog all the GWAS I am interestes in. In this file I ...
gwas snp written 7 months ago by ste.lu40
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Comment: C: Split a sequence in a fastq file
... yeah, definetly. Thanks! ...
written 8 months ago by ste.lu40

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Popular Question 4 months ago, created a question with more than 1,000 views. For Seqtk subseq: structure of file name.lst
Popular Question 7 months ago, created a question with more than 1,000 views. For Install Bowtie2 on Windows 10 Home edition

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