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Question about Bedtools intersect: allows for multiple matches?

bedtools pybedtools written 17 days ago by fr • 100 • updated 17 days ago by jared.andrews07 • 2.3k

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pyBedTools.BedTools.intersect() not working on dataframe

bedtools pybedtools written 27 days ago by fr • 100

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317

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pybedtools intersect using additional options

pybedtools written 5 months ago by zoegward • 60

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381

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Bedtools intersect -u or -wa causing issues

bedtools python pybedtools igv written 11 months ago by alex.v.nesta • 0

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1.4k

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How to count the total aligned bases in BAM?

python bam pysam pybedtools written 12 months ago by vw • 20

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568

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How to compute target aligned reads/total aligned reads (read enrichment) with Python?

bed bam pybedtools pysam written 12 months ago by vw • 20

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685

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pybedtools change fasta headers

python pybedtools written 2.2 years ago by RT • 330

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1.1k

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Use bedtool to get number of shared features from intersetions

bedtools pybedtools written 2.7 years ago by themantalope • 40 • updated 2.7 years ago by Alex Reynolds ♦ 28k

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1.2k

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How do I filter a bam on length with pybedtools?

pybedtools written 3.0 years ago by endrebak • 760 • updated 3.0 years ago by Ryan Dale ♦ 4.8k

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2.7k

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pybedtools.BedTool.intersect not working, install problem

pybedtools written 4.6 years ago by juncheng • 180 • updated 3.8 years ago by Biostar ♦♦ 20

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1.7k

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How do I pass options to pybedtools getfasta

bedtools python pybedtools written 4.3 years ago by geek_y ♦ 9.6k • updated 4.3 years ago by RamRS ♦ 21k

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Recent Replies

C: how can i predict the interface site of RNA with protein by bangbang3332 • 0
![none of them can been used.....][1] [1]: https://ibb.co/8j6Sn4b
C: how can i predict the interface site of RNA with protein by bangbang3332 • 0
thanks for your help , that is really helpful! but i also meet with some problems. i have notic...
C: how can i predict the interface site of RNA with protein by natasha.sernova • 3.4k
1) See this article from 2011, it compares many tools. Predicting RNA-Protein Interactions Using...
A: Unexpected Bowtie2 behavior with --phred64 and --phred33 flags by Devon Ryan ♦ 90k
1. The phred scores are only ever used for computing alignment scores in cases where there are mi...
A: Merging BAM file with Samtools by Devon Ryan ♦ 90k
That's probably a warning (it's written as such, but I haven't looked through the repercussions) ...
C: About qiime :convert fastq to fasta by SMK • 430
You can also use [SeqKit][1]: ``` seqkit fq2fa file.fq.gz -o file.fa ``` or even awk: ``` zcat...
C: Keeping only common variants in the merged VCF file by seta • 1.2k
Many thank for your nice solution.
C: UK Biobank l2r data holds segment means but no segment locations? by Kevin Blighe ♦ 42k
Well, in addition to Ram's comments, at which data are you looking, exactly? - you have provided ...
C: Which are the protein classes by Kevin Blighe ♦ 42k
Boa tarde Carlos, o que significa 'universal protein classes'?
A: How to draw heatmap plot use cnv seg data called by gatk? by Kevin Blighe ♦ 42k
Please ignore `copynumber` and think about the problem some more... Here is what you should do: ...
C: Handling Duplicate Probe Expression Values In Spotted Cdna Microarray by Kevin Blighe ♦ 42k
For some strange reason, I knew that probe 205225_at was *ESR1* (oestrogen receptor alpha 1) with...
C: Bash not finding file by SMK • 430
You're welcome. This is already a new question, please consider posting to a new one.

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