User: m.wekking

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m.wekking10
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m********@students.uu.nl

Posts by m.wekking

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Comment: C: Why does samtools mpileup skip positions?
... Thanks for the quick response! my reads are indeed paired, when you say that the alignment is not marked as proper pair you mean this is not properly marked in the bam file, right? ...
written 7 weeks ago by m.wekking10
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Why does samtools mpileup skip positions?
... So I ran Mpileup on a Bam file i generated, I run the command: samtools mpileup -f hg19.fa file1.bam -o file1_pileup.txt But when I look at this pileup file, it looks like samtools skips certain positions: chr19 1080247 N 2 cc EE chr19 1080257 N 2 cc AA chr19 1080258 N 2 c$c AA ...
samtools mpileup written 7 weeks ago by m.wekking10 • updated 7 weeks ago by Istvan Albert ♦♦ 84k
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Comment: C: BWA aln - failed to locate the index
... That's it! thank you very much! ...
written 12 months ago by m.wekking10
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Comment: C: BWA aln - failed to locate the index
... That's it! thank you very much! ...
written 12 months ago by m.wekking10
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BWA aln - failed to locate the index
... So I have alot of paired-end sequence samples in the formate sample_x_fw.fastq and sample_x_rv.fastq and want to align these with the BWA sampe command so I downloaded the hg19.fasta and ran: bwa index -p bwa_hg19 -a bwtsw hg19.fa this resulted in: - bwa_hg19.amb - bwa_hg19.ann - bwa_h ...
bioinformatics alignment bwa written 12 months ago by m.wekking10 • updated 12 months ago by Pierre Lindenbaum130k
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Finding deferentially active regions with DESeq2
... I have a File that contains certain enhancer regions per chromosome and per region how many reads are found from different samples. The 1 and the 2 stand for the two different groups I have. The original file is tab delimited. I.E.: $ cat enhancers.bed chr | start | end | sample1a | sample ...
R deseq2 chip-seq written 21 months ago by m.wekking10 • updated 21 months ago by shawn.w.foley1.2k
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Comment: C: find overlapping Chip-seq peaks and return outerboundries
... For This current project I have in total 3 different files but for other projects it is possible that I have more than five repeats .. So I need a solution that works for a varying amount of files ... ...
written 21 months ago by m.wekking10
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Comment: C: find overlapping Chip-seq peaks and return outerboundries
... Thank you very much! will this also work if I have more than 2 .bed files? ...
written 21 months ago by m.wekking10
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find overlapping Chip-seq peaks and return outerboundries
... I have .bed files with different peaks and I need to find the overlap, but when two peaks overlap I want the program to return the outer boundries of the two peaks, i.e. $ cat sample1.bed chr1 20 40 chr1 60 80 chr2 80 120 $ cat sample2.bed chr1 17 35 ...
overlap chip-seq written 21 months ago by m.wekking10 • updated 21 months ago by ATpoint38k

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