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compare two groups of multiple bed files

bedtools bedfiles written 16 days ago by blur • 140 • updated 16 days ago by Alex Reynolds ♦ 31k

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117

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getting bed files into R

R haploid data plink bedfiles written 5 months ago by wrab425 • 20 • updated 5 months ago by jordrell • 0

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320

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Bedtools Intersect related

bedtools chip-seq tool bedfiles written 17 months ago by chaudharyc61 • 30 • updated 17 months ago by 2nelly • 220

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734

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Compare a long list of BEDFiles against a whole genome/ chromosome ?

wholegenome bedfiles biopython compare written 4.3 years ago by dearbbhyc • 0 • updated 4.3 years ago by Alex Reynolds ♦ 31k

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1.8k

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How to create Hi-C analysis package HiFive fend object

hi-c hifive python hicup bedfiles written 5.3 years ago by jacel • 0 • updated 5.1 years ago by Biostar ♦♦ 20

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3.4k

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Does multiIntersectBed works with -u and -f parameter?

bedtools intersect bedfiles sequencing written 5.8 years ago by ivivek_ngs • 5.0k • updated 5.8 years ago by Aaronquinlan ♦ 11k

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Recent Replies

C: Obtaining SNPs with large samples in a short time by Kevin Blighe ♦ 68k
These are whole-genome BAMs? Please add more information
A: What happens if a UMI fragment has a PCR artefact? by ATpoint ♦ 42k
That is a common problem in sequencing and specialized software addressing sequencing errors im U...
A: Novel protein identification by Qiongyi • 10
A general guide is: If you find a predicted protein which is not previously documented (e.g. not ...
C: Manipulating a fasta file to only have specificcharacters by Qiongyi • 10
GO TO https://github.com/Qiongyi/custom_PERL_scripts/ AND THEN FIND linker.pl
C: Demultiplexing 10x fastq files by GROUPS of barcodes by bds1217 • 0
`umi-tools` actually worked great and was way easier than I was expecting it to be. I thought I w...
C: What happens if a UMI fragment has a PCR artefact? by _r_am ♦ 31k
Do not add an answer unless you're answering the top level post. Use `Add Comment` or `Add Reply`...
A: What happens if a UMI fragment has a PCR artefact? by asumani • 70
I see. That wrong UMI created during a PCR amplification.And that single read with wrong UMI will...
C: Is there a way to use multiple processors (parallelize) to create a heatmap for by _r_am ♦ 31k
Unfortunately, no. If the package is not designed to use multiple cores, there's not much you can...
C: Creating gtf file? by opplatek • 40
What do you need a gtf for and what kind of information do you think it should contain? Since you...
A: How to convert realign BAM file into fastq file by opplatek • 40
Based on the other comments `samtools fixmate` didn't help so it seems you have some singleton re...
A: SIGNATURE MATRIX IN CIBERSORT by dare_devil • 10
Go through this [paper][1] . They mention about creating custom signature matrix [1]: https:...
C: How to convert realign BAM file into fastq file by opplatek • 40
You obviously lost some of the mates during your processing. My guess is that one of the steps yo...

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