User: a.rex

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a.rex170
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Posts by a.rex

<prev • 110 results • page 1 of 11 • next >
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How to convert Jaspar motif to input into homer?
... I want to use Homer to scan for a particular motif in my genome of interest (under ATAC peaks). This motif is found in Jaspar - how can I convert it to a format suitable for Homer? ...
homer jaspar written 11 days ago by a.rex170
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Is it common for ATAC-peaks to be located in Repeat Masker annotated regions?
... I have ATAC-reads that map to make peaks in repeatMasker + repeat modeller annotated regions? Is this common? Is this an artefact of mapping or perhaps regulatory elements that are transposon derived? ...
genome atac-seq written 11 days ago by a.rex170
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Finding common peaks between F-seq peak region files
... I have 3 biological ATAC-seq conditions, each with two replicates. I have obtained F-seq region peak files for each of the six sample. These are the peak number metrics: sample 1 condition1 = 260388 sample 2 condition1 = 259940 sample 1 condition2 = 292697 sample 2 condition2 ...
fseq atac written 16 days ago by a.rex170 • updated 16 days ago by Alex Reynolds26k
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Find unique non overlapping intervals between two files?
... I have two bed files, and I want to find unique non-overlapping intervals between the two files, given there is less than 30% overlap E.g File 1: interval1 5248 6157 interval2 6200 6393 interval3 6800 7493 ... File 2: gene1 5258 6257 gene2 7800 7993 ...
bed written 17 days ago by a.rex170 • updated 17 days ago by harold.smith.tarheel4.2k
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Using BedTools to look at unique bed intervals between two files
... I have two bed files - they correspond to peak intervals for ATAC-seq of different samples. I want to parse out the peak intervals unique to one file, as well as quantify the similarities between the two files. How can I do this with BedToools? ...
bedtools written 19 days ago by a.rex170 • updated 19 days ago by Alex Reynolds26k
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What should I choose to best specify background sequences when looking for motifs under peaks in Homer?
... I have a file with a set of intervals (corresponding to ATAC peaks) that are within introns or close to a specific type of gene (i.e. stem cell genes). I have another file of intervals for peaks that are within introns or close to another type of gene (i.e. genes expressed in the liver). I wish to l ...
homer written 19 days ago by a.rex170
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Comment: C: Finding motifs with Homer for obscure species.
... Hi - why is this better? ...
written 22 days ago by a.rex170
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Finding motifs with Homer for obscure species.
... I have recently done some ATAC-seq in an obscure invertebrate organism. I have a bed file for peaks that changed under different biological conditions. I have run this through Homer, giving the whole genome as background, and have obtained a list of motifs enriched under these peaks. Problem is, som ...
genome homer atac-seq written 23 days ago by a.rex170
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Fseq versus MACS2 for ATAC-seq
... I wish to compare two biological conditions with respect to their open chromatin. I use ATAC-seq as my assay. My strategy has thus far been to: 1. call peaks on replicates of each condition 2. find common peaks between replicates 3. merge peaks between conditions 4. count reads in peak intervals ...
atac-seq written 25 days ago by a.rex170
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Comment: C: How can I look at find 'open chromatin' from ATAC-seq data using MACS2
... Hello - how exactly do I use this for ATAC-seq. I have a bed interval file made from my mapped reads bam file. What else is the input? An example command would help. ...
written 25 days ago by a.rex170

Latest awards to a.rex

Popular Question 16 days ago, created a question with more than 1,000 views. For Fetching NCBI ID for a list of species?
Centurion 25 days ago, created 100 posts.
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Issues installing bcl2fastq?
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Fetching NCBI ID for a list of species?
Popular Question 3 months ago, created a question with more than 1,000 views. For parse error with samtools
Popular Question 3 months ago, created a question with more than 1,000 views. For Issues installing bcl2fastq?
Student 3 months ago, asked a question with at least 3 up-votes. For mapping reads to repetitive elements in genome?
Popular Question 5 months ago, created a question with more than 1,000 views. For createRepeatLandscape in RepeatMasker
Popular Question 10 months ago, created a question with more than 1,000 views. For Issues installing bcl2fastq?
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Student 22 months ago, asked a question with at least 3 up-votes. For mapping reads to repetitive elements in genome?

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